Chanthupottu movie tells the story of Radhakrishnan (Dileep) an only son, who is brought up like a girl by his grandmother (Sukumari) who wanted a granddaughter. He is known as Radha. He dresses like a girl, wears makeup, thinks and behaves like a girl.
He is comfortable with his identity till he came across Mallu ( Gopika). This young girl confesses that she is in love with him. Mallu, a friend for so long, now becomes his fiancee.
Now he starts feeling uncomfortable with his identity. He wanted to be Radhakrishnan. His struggle to get back his real identity forms the climax.