Legolas, named after an elf in Lord of the Rings, helped researchers understand how the animals hunt together.
The body was found next to a highway along with a shotgun cartridge, in what Cheetah Conservation Botswana called an "unnecessary and unprovoked attack".
The death is being investigated as a poaching case.
It comes after another famous big cat, Cecil the Lion, was killed in Zimbabwe by a US dentist, sparking worldwide condemnation.
Legolas was not posing a danger to livestock because there were no cattle in the area, indicating the animal had instead been shot in an opportunistic attack, CCB said.
The group said it sympathised with farmers who have problems with predators, but described the killing as "needless and heartbreaking".
At 68.5kg in weight, Legolas was one of the biggest cheetahs ever caught.
He and two of the three other cheetahs he hunted with were fitted with collars that CCB said had "revolutionised" the study of the animals' collaborative hunting techniques, which until then had remained largely unknown.
The killing of Legolas means three of the seven cheetahs fitted with collars for the research project have been shot.
The estimated population of 10,000 wild cheetahs in Africa today is classified as 'vulnerable' in the IUCN's Red List of threatened species.

The NHS spent £8.84m on private ambulances in the capital last year compared to £795,000 in 2011, according to Freedom of Information data.
The London Ambulance Service (LAS) conceded it was losing staff due to "pressure on the organisation".
But LAS denied claims it had employed private staff previously sacked by the NHS.
Heidi Alexander, Labour MP for Lewisham East, claimed London ambulances were taking "on average two minutes longer than three years ago" to respond to the most serious call-outs.
Labour said its research discovered private ambulance usage by ambulance trusts across the country grew by 82% between financial years 2011/12 and 2013/14, from £37m to £67.5m last year.
Private ambulance spending In Yorkshire and the North East more than quadrupled to hit £3.56m and £2.9m respectively, said Labour, although other ambulance services maintained low spending during the two years, while one trust reduced its reliance on private vehicles.
Shadow health minister Jamie Reed raised concerns over the figures and the "increasing use" of private ambulances during health questions in the House of Commons.
But his comments were branded "absolute nonsense" by public health minister Jane Ellison, who said that previous Labour government "occasionally deployed private ambulances too".
Brendan Kemp, regional organiser for the GMB union, questioned the hiring practices of ambulance trusts and their ability to keep staff.
"Who's checking the qualifications of the staff that man these vehicles?" he said on BBC London 94.9.
"Often staff that have been dismissed by London Ambulance Service for something, often they'll reappear working for a private contractor."
But Jason Killens, director of operations for the LAS, said every private contractor "is checked by us before we use them".
"Staff that leave the LAS for reasons of clinical safety would not be redeployed on those private contracts with us," he told BBC London 94.9.
Mr Killens said increasing demand each year "is adding pressure in the organisation" and conceded that "some staff leave" as a result, with about 500 vacancies currently unfilled.
He added: "There is a small number that leave us and go and work in the private sector, but the vast majority of people that leave the ambulance service in London go to work elsewhere in the NHS."
A Botswanan cheetah called Legolas that was being studied by researchers has been killed, conservationists said.
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Spending on private ambulances in London grew by 1,000% between 2011 and 2013, the Labour party has claimed.