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If I want to say only 日本 in a sentence then each character is pronounced in
its onyomi version isn't it? If this is an exception and one (or all) of the
characters is not pronounced in onyomi version then ok i'll remember the
exception, but 日 isn't pronounced "ni" anyway. So how can I understand this
situation?
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2019-08-20T08:47:07.010
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kanji pronunciation
Why is 日本 read as "nihon" but not "nitsuhon"?
There are three readings for 日本: にほん, にっぽん, and やまと. The last reading is non-
standard as far as general use. The first two are still used often, but にほん is
by far the de rigueur reading currently.

Possibly you are reading something old, where 日本 is written as につぽん. While
today, a repeating consonant is written with a small tsu (っ), in the past it
was often written with a regular-sized tsu (つ), and some elderly people still
write it this way. What looks to you like **_Nitsuhon_** is actually
**_Nippon_**.

日 has several readings, but the reading of に in にほん is a special case and
shouldn't be applied outside of this circumstance.
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(First, 日本 is pronounced like _nippon_ or _nihon_ , but not _nitsuhon_.)

Unfortunately, there are tons of irregularities and exceptions regarding the
readings of words, and you have to master them individually, word by word.
Pronunciations change over time, but spellings tend not to change. In the case
of Japanese, there are even kanji words that completely ignore the original
pronunciation of each kanji (known as jukujikun). For example 一日 is read ついたち.

  * [日曜日，the different meanings and pronunciations of 日](https://japanese.stackexchange.com/q/68850/5010)
  * [Where does the な in 大人 (otona) come from?](https://japanese.stackexchange.com/q/24513/5010)
  * [Why is 一日 'tsuitachi'?](https://japanese.stackexchange.com/q/53068/5010)

Uncommon words tend to exhibit less exceptions, so you don't need to suffer
forever. English is [one of the worst European
languages](https://www.quora.com/In-what-languages-besides-English-are-
spelling-and-pronunciation-very-different-and-why) in terms of spelling-
phonetic consistency, so if you can speak English, you can master Japanese :)
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There are no strict rules for how a word written in kanji translates to
reading. There are rule of thumbs, but they do not give a strict indication.
At best, they will give you a 40% chance to correctly guess a word's reading
from its kanji. Which isn't trivial, but far from reliable.

Most of the stuff you've learned about onyomi or kunyomi is basically useless
in practice, as words that actually follow those rules in a predictable way
are actually in the minority. If you try to look at words that "don't follow
the rules", or where the rules are ambiguous, as exceptions, you'll find that
most of the Japanese language is made of exceptions.

Words like 今日, 昨日, 相応しい, or 大人しい, are great examples for having no clear
relation between the kanji and reading. Even when a single kanji is used, you
have examples like 全う, 全て, and 全く, all having completely different readings.

Even when a kanji has the same reading in multiple words, it can still have
multiple options. For instance, in 男性, 可能性, 性質, 事件性, and 個性, 性 would be read
as "sei". While in 本性, 性分, 相性, and 性根, 性 would be read as "shou". So even when
it seems to "follow the rules", you're still getting a 50:50 guess on the
reading.

日本 is actually closer to the latter case. 本 is quite often read as "hon"
(while occasionally also being "moto"). 日 is most often "hi", "jitsu", or
"nichi". The latter lends itself to both the reading "nippon", as in "nichi"
with "chi" shortened to a small "tsu", followed by "hon" with "ho" upgraded to
"po", similar to in 一本. "nihon" can be seen as farther shortening "nichi", or
as doing something that is between "nichi" and "hi".

But really, if you're hoping to read any given word, you should learn the
reading of the whole word, not try to divide it into kanji. After learning
enough words, you will sometimes be able to spot kanji which are read the same
in multiple words, and be able to use that to guess the reading of new words.
But even then, it's anywhere between a 50:50 to 1 in 5 guess, and if you don't
know the word, you'll have to look up its correct reading anyway. Kanji
reading will serve, at best, as a hint or mnemonic.
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2019-08-20T19:19:53.157
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You're right, `日本` pronunciation is based on the on-yomi of each kanji.

`本` has only one on-yomi : "hon", so no problem here. `日` has
[two](https://dictionary.goo.ne.jp/word/kanji/%E6%97%A5/) though : "nichi"
([go-on](https://en.wikipedia.org/wiki/Go-on)) and "jistu" ([kan-
on](https://en.wikipedia.org/wiki/Kan-on)).

You can "understand the situation" of `日本` being nowadays read "nihon" or
"nippon" through its history :

  1. it is thought to have evolved from the go-on reading "nichihon" ( **ニ** チ **ホン** ) to "nippon" ( **ニ** ッ **ポン** ) through phonetic change (called [gemination](https://en.wikipedia.org/wiki/Gemination) or [促音便](https://ja.wikipedia.org/wiki/%E9%9F%B3%E4%BE%BF#%E4%BF%83%E9%9F%B3%E4%BE%BF))
  2. and then from "nippon" to "nihon" for pronunciation softening.

Nowadays both "nippon" and "nihon" readings have been retained and are
commonly used.

Incidentally, the kan-on reading of 日本, `ジツホン` (jitsuhon), is thought to be at
the origin of its translations in a bunch of foreign languages (Marco Polo's
"Cipangu", "Jipang", "Japan", etc).

_Source:[大辞泉](https://dictionary.goo.ne.jp/jn/167553/meaning/m1u/)_

* * *

About your question and initial thought process:  
I think your kanji app shouldn't have listed "nitsu" as an on-yomi for `日` :
`日` is sometimes read `ニッ` but as a gemination from `ニチ` so really that's the
same one on-yomi.  
Building on expecting `日本` to be read with the on-yomi of its kanji, and
gemination being omnipresent in modern Japanese, you should have expected it
to be possibly read "nippon" or "jippon".  
Only remains "nihon", which indeed is an oddity and warrants a question here.
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