The work aims to introduce the cognitive development theory to summarize the principles of children's popular science APP interface interaction design based on children's cognitive ability and acceptance characteristics, and verify these principles through design practice to improve the user experience of children, so that children's popular science APP can better play the auxiliary role of scientific enlightenment. The development and use status of children's popular science APP were analyzed through case analysis method combined with questionnaire survey method, the pain points of children in the using process were summarized, and the strategy of interface interaction design of children's popular science APP based on children's cognitive ability and acceptance characteristics was put forward, and applied to the design practice. Finally, the design effect was verified and analyzed through interviews. Through design practice and design evaluation, it can be seen that the integration of cognitive development theory into the interface interaction design of children's popular science APP has a positive effect on improving known design problems and enhancing children's use effect, which can reduce children's discomfort and the probability of misoperation to a certain extent, and also improve children's sense of participation and emotional experience.