Based on the total factor productivity perspective (TFP), this paper uses DEA model and Malmquist index to evaluate the development quality of strategic emerging industries in China from 2001 to 2015. The results show that the annual average growth rate of TFP in China’s strategic emerging industries is 13.4%, which shows an upward trend, but the TFP growth rate showed a fluctuating trend of decline, and the gap between provinces is narrowing. Technological progress is the most important factor to promote TFP growth. The TFP growth rate in the central region is higher than that in the west, east and northeast respectively. The TFP growth rate in the eastern and western regions mainly rely on technological progress, while that in central and northeast regions mainly rely on technological efficiency improvement, and the scale diseconomy in the northeast region is the most prominent problem. The gap between TFP in central, western and eastern inner provinces is gradually narrowing, while that in the northeast is expanding.