<p>The new round of industrial change led by biomedicine has highlighted the characteristics of innovation networks, such as interaction and complementarity of multiple subjects and interweaving of multiple factors. This intensifies the dual demand for network heterogeneity and multidimensional proximity in industry-university-research cooperation (IURC) institutions. Based on the dual perspective of network heterogeneity and multidimensional proximity, this paper empirically investigates the multifactorial influence mechanism of cooperation innovation performance of industry-university-research (IURCip) based on the collaboration patent data of China’s biomedical industry in the last decade. The results show that: (1) network heterogeneity positively affects IURCip, and geographic proximity negatively moderates the relationship between network heterogeneity and IURCip; (2) there is an inverted “U”-shaped relationship between technological proximity and IURCip, but geographic proximity does not present a significant negative moderating role in the relationship between technological proximity and IURCip; (3) geographical proximity has a significant negative effect on IURCip; (4) technological proximity and geographic proximity have different effects on IURCip at different stages of industrial innovation networks.</p>