Ryouta Kajiyama is a new deliveryman working for Kaizuka Delivery Services. On his route, one particular customer stands out: Mamoru Aizawa, a tall man living in apartment 411 who always answers the door wearing a large rabbit head. Aizawa is a recluse who speaks very little and seems to have almost no direct contact with the outside world, relying on frequent deliveries for his daily needs.

Initially, Ryouta finds the situation bizarre and unsettling, letting his imagination run wild with theories that the man might be a criminal or a pervert. Despite these suspicions, the deliveryman cannot ignore the timid and gentle way Aizawa speaks to him. One day, the bunny-headed man nervously grabs Ryouta’s arm and awkwardly asks him to continue delivering his packages, an act that begins to melt Ryouta's fear and replace it with curiosity.

The story is set in a contemporary Japanese town, revolving around the growing connection between the friendly and straightforward deliveryman and his deeply reclusive customer. The central conflict stems from Aizawa's extreme social anxiety and shyness, which is the true reason he hides behind the rabbit mask. He is not a criminal but a hikikomori who finds normal human interaction nearly impossible, and the mask allows him a degree of comfort. As Ryouta makes more deliveries, he discovers that Aizawa works from home creating crafts with flower petals, which explains the origin of the manga's title, Hana to Usagi (Flower and Bunny). The narrative arc follows their tentative relationship as Ryouta accidentally sees Aizawa's bare face and the two men navigate their feelings for one another, moving from a professional relationship to a romantic one while dealing with Aizawa's overwhelming anxiety.

The collected volume also includes two one-shot stories: Ano Egao wo Mou Ichido and Bokura no Saidai Kouyakusuu, which feature separate characters and scenarios unrelated to the main plot about the deliveryman and the bunny-headed man.