R&D investment is considered to be an important factor to enhance the competitiveness of enterprises. Based on the data of 92 listed companies in pharmaceutical manufacturing industry from 2012 to 2021, the evaluation index system of enterprise performance was established. Then using the principal component analysis, the comprehensive enterprise performance score was calculated. And the regression analysis was used for studying the impact of R&D intensity on enterprise performance. The results show a significant negative correlation between R&D intensity and the current enterprise performance. But R&D intensity lagging behind three years or four years has a significant positive effect on improving enterprise performance.The results can provide support for pharmaceutical manufacturing enterprises to optimize structure of the R&D investment and help the government to adjust or formulate policies on R&D and innovation.