In view of the phenomenon that some e-commerce enterprises in china are operating at a deficit and their net income is negative, a dynamic BP-SBM DEA model with two-stage structure that can hand negative evaluation index is constructed to evaluate the comprehensive performance, production operation performance and capital operation performance of 47 listed e-commerce enterprises from 2017 to 2019. The main conclusions are as follows: the overall performance of China"s listed e-commerce enterprises is relatively low, the overall performance of same type enterprises differs greatly, and the overall performance of the individual enterprise fluctuates greatly; the performance of production operation of listed e-commerce enterprises is generally higher than that of the capital operation stage, and the inefficiency of overall operational performance mainly originates from the capital operation stage; among retail e-commerce, industrial e-commerce and cross-border e-commerce, retail e-commerce has the highest capital operation performance, while cross-border e-commerce has the lowest production operation performance; Only a few enterprises have high production and operation performance and high capital operation performance. Therefore, China"s listed e-commerce enterprises should strive to improve their comprehensive operation level and pay attention to the coordinated development of production operation performance and capital operation performance.