OBJECTIVE：To provide referen ce for promoting innovation cooperation of pharmaceutical manufacturing industry among regions and building a more perfect and close pharmaceutical innovation cooperation network. METHODS ：Based on China ’s pharmaceutical manufacturing cooperation patent data published by the State Intellectual Property Office ，the main cross-region cooperation patents among 31 provinces，autonomous regions and municipalities in China in 2016 were extracted ；based on literature review ，some hypotheses were put forward about the factors that may affect the cross regional innovation cooperation of Chinese pharmaceutical manufacturing industry. Taking the provincial R&D cooperation intensity as the dependent variable and the above influencing factors as the independent variables ，QAP analysis method was used to establish the model for data analysis. RESULTS & CONCLUSIONS ：Differences in regional economic GDP ，geographic distance ，economic distance ，technical distance，and whether Beijing or Shanghai are involved in the cooperation area all have an impact on cross-regional innovation cooperation in the pharmaceutical manufacturing industry. Large regional economic GDP difference is conducive to promoting cooperation. Developed regions represented by Beijing and Shanghai have strong radiating effects and can significantly promote cooperation. Geographical distance and economic distance have a negative effect on cross-regional innovation cooperation in pharmaceutical manufacturing ，while technological distance has positive effect.