The pharmaceutical industry is an important industry for the national economy and the people's livelihood, which is not only beneficial to the people's livelihood, but also has huge commercial value. How to promote the development of Chinese pharmaceutical industry is an urgent problem to be solved. In this study, 47 listed pharmaceutical companies are taken as cases, and Qualitative Comparative Analysis of Fuzzy Sets (fsQCA) is used to analyze the influence of five antecedent conditions on the total factor productivity of pharmaceutical enterprises from the perspective of corporate governance, and to explore the composition to Total Factor Productivity (TFP) improvement. The results are as follows. First, single corporate governance factor does not constitute the necessary condition to improve the TFP of pharmaceutical enterprises. Second, there are three configurations of high TFP of pharmaceutical enterprises, among these, two configurations belong to regulatory constraints type and one configuration belongs to the active board type. There is only one configurations to low TFP of pharmaceutical enterprises: the passive board. Based on the perspective of configuration, this paper discusses how corporate governance drives TFP improvement in pharmaceutical enterprises, which can provide systematic thinking and practical guidance for each company to promote its TFP improvement according to its own corporate structure.