Interdisciplinary scientific research method plays a significant role in promoting technological innovation. As the principal subject in scientific research activities, college students need to improve their innovation ability using interdisciplinary knowledge resources and knowledge network. Existing researches are mostly carried out from a single perspective of knowledge network, and ignore systematical analysis for interdisciplinary multilayer network. For that reason, the influence mechanism of structural characteristics of interdisciplinary knowledge network on college students’ innovation ability is established in this article. An interdisciplinary-dependent multilayer network is built and network nodes are divided into interdisciplinary knowledge elements, scientific research theme, and discipline and specialty. Structure attribute of interdisciplinary knowledge network and relationship attribute of interdisciplinary knowledge elements are also used to calculate indicators at different knowledge dimensions, and specific indicator measurement modes are proposed. The regression model is built to explore direct influence mechanism of dynamic and static characteristics of interdisciplinary knowledge network on college students’ innovation ability. A regression model is also built to further verify the regulating effect of disciplinary knowledge’s network location attribute of college students’ specialty in influence relationship between interdisciplinary knowledge network and college students’ innovation ability. Last, corresponding analysis result is given based on experiment result.