As a high-tech industry, the pharmaceutical industry in China is uncompetitive and is difficult to go further. By evaluating the innovating capability of different pharmaceutical companies, this paper attempts to find the key factors affecting the innovating ability and provides suggestions for pharmaceutical companies to improve the innovating capability. The research indicates: Independent innovating factor and policy-influencing factor are two factors and the key factors affecting the innovating capacity of different pharmaceutical companies are different; the ability of independent innovation is the key influencing factors to the state-owned pharmaceutical companies, while policy- influencing factor plays a key role in foreign-invested pharmaceutical companies.