Abstract:: Constructed a kind of new network DEA model. Two-stage network DEA model was combined with Malmquist index to measure technical innovation efficiency’s change of pharmaceutical manufacturing on Chinese various provinces from 2006 to 2014,and based on this analyzed its influences by Sys-GMM. We found that technical innovation efficiency of Chinese pharmaceutical manufacturing is on the up trend and its differences between regions are high. The growth of TFP is due to technical efficiency, while technology has no progress. Market structure, the level of human capital, openness degree, R&D strength and growth ability has a significant positive effect on pharmaceutical manufacturing innovation efficiency, while Enterprise scale, the level of economic development have a significant negative effect on it ,and government’s support have no significant effect on it.