Abstract:As a national strategic emerging industry, the bio-pharmaceutical industry has been hailed as the most promising high-tech industry in twenty-first Century, but compared with the developed countries (even in other parts of China), the bio -pharmaceutical industry in Hubei faces the fact that the overall technical level of the industry is not high and the competitiveness is so weak. It is an urgent task to solve the problem of restricting the innovation and development of Hubei''s bio- pharmaceutical industry, and to choose the proper way of industrial innovation development and proper system arrangement. This paper uses two stage data envelopment analysis correlation analysis of transverse and longitudinal analysis of the development level of the development trend of bio pharmaceutical industry in Hubei province innovation efficiency method, found that the current scientific and technological achievements into the efficiency of research and development of bio pharmaceutical industry in Hubei stage or the two stage than the other area in a certain gap, a serious lack of efficiency; From its own development point of view, high efficiency technology research and development, but the lack of scale efficiency, especially the transformation of scientific and technological achievements stage both technology efficiency and scale efficiency is not high, this is the key bottleneck restricting the development of bio pharmaceutical industry in Hubei. On this basis, several measures and suggestions for enhancing the efficiency of industrial innovation are put forward for reference by the government.