"Cat Girls Garden" is a manga series that centers around a young man named Haruto, who unexpectedly inherits a small, rundown café from his late grandmother. Upon arriving at the café, he discovers that it is inhabited by a group of anthropomorphic cat girls, each with distinct personalities and quirks. These cat girls, who refer to themselves as "Nekos," are not ordinary animals but rather magical beings capable of human speech and interaction. They have been living in the café for years, maintaining it in their own unique way, though their efforts often lead to comedic mishaps due to their lack of understanding of human customs.

The café, named "Cat Garden," is a place where humans and Nekos coexist, though it has fallen into disrepair over time. Haruto, initially overwhelmed by the responsibility, decides to take on the challenge of reviving the café with the help of the Nekos. Each Neko has a specific role in the café, such as cooking, cleaning, or entertaining customers, but their inexperience and playful nature often create humorous and chaotic situations. The series explores the dynamics between Haruto and the Nekos as they work together to restore the café to its former glory.

The main Nekos include Mikan, a cheerful and energetic orange tabby who often takes the lead in their antics; Shiro, a calm and intelligent white cat who serves as the voice of reason; and Kuro, a shy and reserved black cat who is often overshadowed by her more outgoing companions. Other Nekos, such as the mischievous twins Choco and Vanilla, add to the lively atmosphere of the café. As the story progresses, Haruto learns more about the Nekos' origins and the magical world they come from, which adds depth to the narrative.

The plot unfolds through a series of episodic adventures, with each chapter focusing on a different challenge or event at the café. These range from preparing for a local festival to dealing with rival businesses or unexpected visitors. The interactions between Haruto and the Nekos highlight themes of friendship, responsibility, and the importance of understanding and accepting differences. The series balances lighthearted comedy with moments of heartfelt emotion, creating a narrative that appeals to a wide audience.

As the café gradually gains popularity, Haruto and the Nekos face new challenges, including the arrival of other magical beings and the need to protect their unique way of life. The story maintains a focus on the growth of the characters and their relationships, with Haruto becoming more confident in his role as the café's caretaker and the Nekos learning to navigate the human world more effectively. The series concludes with the café thriving as a beloved community hub, symbolizing the harmony between humans and magical beings.