E-commerce has had a huge impact on the business pattern of the physical supermarket. However，as the large chain supermarkets, their growth have not fallen back. At the same time, the original BCC model to analyze the panel data also has the disadvantage of ignoring technological progress. Therefore, in order to explore accurately the operational efficiency of them in the trend of rapid development, this paper uses the generalized DEA method to measure China 15 large chain supermarkets operational efficiency during 2008-2015. The results show that the average comprehensive efficiency of these 15 enterprises is fluctuating, and the pure technical efficiency is increasing year by year. Finally, this paper puts forward some reasonable suggestions for improving operational efficiency of the large chain supermarkets.