Using the stochastic frontier analysis method, this paper calculates and analyses the energy efficiency and its influencing factors of China's 30 manufacturing sub-sectors from 2003 to 2010. The following conclusions are found. The overall total factor energy efficiency of China's manufacturing industry is low, only average of 0.3504. There are many energy conservation and emission reduction pressures in manufacturing industry. In the same year, the energy efficiency of different manufacturing sub-sectors is at the relatively fixed level. But the energy efficiency has been rising with the passage of time. The average size of company, total profits and industry concentration would promote the energy efficiency in a certain extent. While property system has brought negative impact on energy efficiency in some degrees.