In recent years, China’s physical retail enterprises have encountered operational difficulties. It is of practical significance to explore the operational efficiency level of physical retail enterprises and its influencing factors in the new era. Based on the questionnaire data of retail stores from 2007 to 2016, this paper uses different models, such as stochastic production frontier and stochastic cost frontier, to test the characteristics of the production function in retail enterprises under two input factors of business area and number of employees, such as return to scale, output elasticity and scale economy, and at the same time to test the effects of the competitiveness of retail stores business circles, the store operation history, commodity turnover days, daily trading volume and unit price on the operational efficiency of stores. The results show that the real retail enterprises in China are in the stage of constant returns to scale, and the operation efficiency of specialty stores and department stores is higher, while the operation efficiency of supermarkets and shopping centers is lower; and the operation history of stores, daily trading volume and unit price have a positive impact on the operation efficiency of stores. Finally, management suggestions are put forward for the store operation of physical retail enterprises.