"Survive! Inside the Human Body" is an educational anime that combines science and adventure to explore the intricacies of human biology. The story centers on three children—Kanna, Futoshi, and Taeko—who are accidentally shrunk to microscopic size and find themselves navigating the inner workings of the human body. Their journey begins when they enter the body of their friend, Hiroshi, through his mouth, setting off a series of explorations through various bodily systems, including the digestive, circulatory, respiratory, and nervous systems.

Each episode focuses on a specific organ or system, with the children encountering personified cells, bacteria, and other microscopic entities that explain their functions and roles in maintaining health. For instance, red and white blood cells are depicted as workers and soldiers, respectively, while harmful bacteria and viruses are portrayed as antagonists threatening the body's well-being. The children must work together, using their newfound knowledge of biology, to overcome challenges and find a way to return to their normal size.

The narrative is driven by a blend of scientific facts and imaginative storytelling, making complex biological concepts accessible to younger audiences. The characters' interactions with the microscopic world are both informative and engaging, as they learn about topics such as digestion, oxygen transport, immune responses, and neural communication. The series emphasizes teamwork, problem-solving, and the importance of understanding how the human body functions.

Throughout their journey, the children face various obstacles, such as battling infections, navigating the bloodstream, and repairing damage caused by external factors. These challenges are often resolved through cooperation and the application of scientific principles, reinforcing the educational aspect of the series. The anime concludes with the children successfully exiting Hiroshi's body, having gained a deeper appreciation for the complexity and resilience of human biology.