In order to scientifically evaluate the impact of the COVID-19 on the operation efficiency of Chinese port cold chain, based on data envelopment analysis (DEA) , also considering the differences of evaluation indicator data and the relationships between the indicators, an improved DEA model was obtained by combining the coefficient of variation method and correlation coefficient method with the DEA model. Taking the impact of the COVID-19 on the cold chain operation of Chinese ports as a example, the improved DEA model and spatial autocorrelation model were used to analysis. Results show that during the COVID-19, the operating efficiency of the cold chain of the important coastal ports in China was characterized by falling first and then rising, and the operating efficiency of the cold chain in other ports was reduced to a minimum during the transmission and outbreak period of COVID-19 except Lianyungang port. Before and after the outbreak of COVID-19, each port in the Moran index scatter chart was located in the second and fourth quadrants, although the cold chain business volume of Dalian port, Ningbo-Zhoushan port and Guangzhou port increased significantly during the impact growth period of the COVID-19, the competition pattern of port cold chain business did not change significantly. The rapid prevention and control measures taken by the Chinese government have had some impact on the cold chain business of port foreign trade, especially the frequency and degree of impact on Dalian Port and Shanghai Port. However, from a long-term perspective, the  strong control measures are important for controlling the epidemic spread risk in port areas, maintaining port operating stably for a long time, and ensuring the normal operation of trade activities.