The aim of the article was to clarify the factors affecting the investment in cooperation and innovation in different sub-sectors of China's pharmaceutical manufacturing industry and its mechanism of action, and provide a reference for improving the level of investment in this field. Based on the relevant indicator data of different sub-sectors of China's pharmaceutical manufacturing industry from 2009 to 2019, the factor analysis method is used to empirically analyze the impact of the summarized factors on the investment in cooperative innovation. It was found that internal investment in research and development funds, investment in scientific and technological activities, investment in new product development, profitability, effective invention patents, and government funding all have a positive impact on investment in cooperative innovation in different sub-sectors of China's pharmaceutical manufacturing industry. Their impact on biopharmaceutical manufacturing industry is greater than that on chemical manufacturing industry, followed by the Chinese patent medicine manufacturing industry. Whereas the degree of enterprise openness has a negative impact on the investment in cooperation and innovation in different sub-sectors of the Chinese pharmaceutical manufacturing industry.