"Kanojo ga Kanji o Suki na Riyū" centers on the relationship between two high school students, Koyomi Kanji and Yuki Shiina, whose lives intertwine through their shared interest in kanji characters. Koyomi, a reserved and studious boy, has a deep passion for kanji, often finding beauty and meaning in their intricate strokes and historical origins. Yuki, a cheerful and outgoing girl, initially approaches kanji as a way to improve her academic performance but gradually develops a genuine appreciation for the art and complexity of the characters.

The narrative explores their growing bond as they collaborate on a school project focused on kanji. Through their interactions, Koyomi and Yuki discover parallels between the structure of kanji and the dynamics of their own relationship. The series delves into themes of communication, self-discovery, and the ways in which shared interests can bridge personal differences. Supporting characters, such as classmates and teachers, contribute to the story by providing additional perspectives on kanji and its cultural significance, as well as influencing the protagonists' development.

The plot is structured around key moments in their academic and personal lives, including school festivals, exams, and extracurricular activities, all of which are tied to their exploration of kanji. The series balances lighthearted moments with introspective scenes, creating a narrative that is both engaging and thought-provoking. By the end, Koyomi and Yuki’s journey highlights the transformative power of understanding and connection, both in language and in relationships.