Based on the business data of 16 listed companies with core business involving cold-chain logistics from 2016 to 2019, by selecting the main business cost, research and development investment, research and development personnel percentage, fixed asset investment as input index, with the main business income and net income as output index, the four aspects of comprehensive efficiency, pure technical efficiency, scale efficiency and input and output were taken for DEA model analysis of the actual operating conditions of the sample enterprises. The results showed that the technological level was the key factor affecting the enterprise operation efficiency, followed by management mode and enterprise operation scale. Finally, the common operating problems of the sample enterprises were pointed out and some comprehensive suggestions to improve the operating efficiency were put forward.