Based on local universities’ scientific research input and output data from 2006 to 2015 in 28 provinces of China，this paper measured the change of scientific research efficiency of the local universities with the method of DEAMalmquist productivity index. The results show that the total factor productivity of scientific research in the local universities increases 2.1% annually，of which technological progress is the main driving force. At present，the efficiency of scientific research in the local universities in China shows a fluctuating state. The proportion of the local universities with increasing research efficiency is 46%，and the overall research efficiency needs to be improved. The efficiency of scientific research among the local universities in different regions varies greatly and presents an imbalance among regions.