Abstract: To explore the relationship between innovation input and innovation output in China's pharmaceutical manufacturing industry, and promote the rational allocation of innovation resources. Based on the relevant statistical data from 2001 to 2019, the SVAR model was constructed, and the impact of innovation input variables such as R&D funds, R&D personnel, product development funds on the number of patent applications and new product sales revenue were empirically analyzed by using impulse response function and variance decomposition methods. The results showed that there was a long-term equilibrium relationship between innovation input and innovation output variables, and innovation input had a positive impact on innovation output, of which R&D investment had the largest contribution, and R&D personnel and product development investment had a certain lag in the impact of innovation output. Therefore, it is necessary to increase investment in R&D funds, R&D personnel and product development funds, improve R&D financing policies, create a good innovation environment, introduce and cultivate scientific and technological talents, improve the output efficiency of innovation input, and promote the modernization of China's pharmaceutical manufacturing industry.