Abstract: Based on the panel data of China's 30 provinces during 2000—2009, the study carries out an empirical analysis on the provincial innovation efficiency and its affect factors by using the DEA model. The results are as follows: during the review period, there was greater volatility in provincial innovation efficiency; while Beijing and Shanghai realized innovation efficiency every year, the rest of the provinces displayed differences in innovation efficiency. As to the affect factors of the provincial innovation efficiency, government investment, talent reserve, regional economy, and opening up had obvious positive effects in the promotion of provincial innovation efficiency, while financial support, industrial structure and infrastructure demonstrated no obvious influence on provincial innovation efficiency.