Bharathan's films were known for their realistic portrayal of rural life in Kerala. Melodrama and escapism, often an integral part of mainstream cinema in India, were usually absent in his films. He also managed to steer clear of the "star-centric" culture, prevalent in Indian cinema, throughout his career. His later films did involve major movie stars but usually without compromising on plot or narrative. Bharathan, along with Padmarajan and K. G. George were largely responsible for introducing a counter culture of meaningful mainstream cinema which often tread the middle path between art-house and commercial cinema. This movement was often called the "middle of the road cinema". Bharathan's films were known for their visually appealing shot compositions. His background as a painter enabled him to create frames that were often credited for their visual beauty. Natural props and nature itself often became important characters in his films (like the railway track in "Paalangal", or the sea in "Amaram"). Bharathan is one of the few Indian directors known to use an elaborate story-board system for filming. He also often designed the posters for his films.

Several of his early films were known for their bold portrayal of sexual themes.His films often defied social conventions and norms about man-woman relationships. "Rathinirvedam" was the sexual-coming-of-age story of the relationship between a teenager and an older woman while "Chaamaram" dealt with the tumultuous affair between a student and his college lecturer. In "Kaatathe Killikoodu" an elderly, married Professor falls for his student. "Kaathodu Kaathoram" was about the social ostracism of a woman who has an adulterous relationship.

The latter half of Bharathan's career saw a distinct change in film making style characterized by a wider canvas,more attention to detail with more distinct focus on narrative style (e.g., "Vaishali", "Amaram", "Thaazhvaaram", and "Thevar Magan"). Some critics argue that this quest for technical excellence was at the expense of the quality of thematic content. Films like "Vaishali" and "Amaram" (where he collaborated with acclaimed cinematographer Madhu Ambat) set a new benchmark for cinematographic excellence in Malayalam and Indian Cinema. "Thaazhvaaram" was stylistically inspired by Classic Hollywood Westerns though the theme and backdrop were distinctly original.

His last few films ("Padheyam", "Chamayam", "Devaraagam") did not receive much critical acclaim or commercial success.

Early career
Style and themes
Trivia
Later life