As a new learning method rooted in the Internet and big data, knowledge graph can exercise people's sensitivity and activity of thinking, and plays an important role in cultivating students' innovation ability. However, at present, there are few studies on the combination of knowledge graph and innovation ability. Therefore, this study chooses to combine knowledge graph with college physical education (P.E.) students' innovation ability to carry out research in the field of education. In college P.E., by analyzing the factors that restrict the cultivation of students' innovative ability, this paper puts forward some methods to cultivate students' innovative ability, such as changing educational concepts, innovating teaching contents and teaching methods, adjusting evaluation methods, and innovating teaching modes, to make students become high-quality talents with all-round physical and mental development and the needs of modern society. Therefore, it is necessary to continuously deepen the educational reform, so that students can continuously improve their interest in P.E. and their innovative ability can be stimulated to a greater extent.