Kaana Kanmani revolves around a happy-go-lucky family comprising Roy (Jayaram), Maya (Padmapriya) and their only daughter Anakha (Baby Nivedita). Roy belongs to a pukka Christian family, while Maya is a Brahmin. The film begins with rib-tickling 'clashes' between Roy's father (Vijaya Raghavan) and Maya's grandmother (Sukumari) in the name of their differences in caste and religion.
After establishing the characters in the first 30 minutes, the story reveals its true nature by slowly exposing the mysterious behaviour of Anakha. During a small function at her residence, the nine year old girl suddenly goes missing. She is finally found on the edge of a flat on the 30th floor, pretending to commit suicide. However, she is saved in time.
The story takes a major turn when Roy decides to go with family for a holiday abroad. But Anakha has a different plan about the tour; she forces her parents to visit their old house in a remote village instead. Giving full support to his daughter's choice, Roy decides to spend a few days in his old house to satisfy her. But when they reach the old home, supernatural events begin to happen.
Anakha shows obvious symptoms of being affected by a supernatural entity (a ghost) and threatens her parents with her magic, revealing a flashback story in which Roy and Maya aborted their first child during their early years to avoid financial instability. Roy and Maya slowly realize that their aborted child is the "ghost" behind Anakha's strange behaviour and ultimately wants to avenge Roy and Maya by killing their sweet Anakha. How Roy and Maya manage to save their child from their "invisible child" forms the rest of the film. Kaana Kanmani is a never-told, heartbreaking story of invisible children, being aborted from millions of wombs at hospital tables every day.