"Kanna-san Daiseikō desu!" centers on Kanna, a high school student who is exceptionally skilled in academics, sports, and social interactions, earning her the admiration of her peers. Despite her seemingly perfect life, Kanna harbors a secret: she is deeply insecure about her height, which she perceives as unusually tall for a girl. This insecurity becomes a recurring theme as she navigates daily life, often leading to humorous and relatable situations.

The narrative explores Kanna's interactions with her classmates, particularly her best friend, Miki, who is shorter and more carefree. Miki often teases Kanna about her height but remains a supportive and loyal companion. Another key character is Hiroshi, a classmate who develops a crush on Kanna. His attempts to confess his feelings are frequently thwarted by Kanna's obliviousness and her preoccupation with her height.

Throughout the series, Kanna's height becomes a focal point for both comedic and heartfelt moments. Her struggles with self-acceptance are balanced by her determination to excel in other areas of her life. The manga delves into themes of self-esteem, friendship, and the pressures of societal expectations, all while maintaining a lighthearted tone. The story progresses through episodic chapters, each highlighting different aspects of Kanna's life, from school events to personal challenges, ultimately painting a well-rounded portrait of her character and growth.