Abstract: Taking 31 provinces, regions and cities of our country as the research object, the cold chain logistics efficiency of fresh agricultural products in China is measured by three-stage DEA model with the provincial panel data from 2012 to 2019. The research results show that, the cold chain logistics efficiency of fresh agricultural products in China is increasing year by year, the cold chain logistics industry of fresh agricultural products in most regions is in the stage of increasing scale efficiency; the informatization level, the infrastructure construction level, the degree of opening to the outside world, and the innovation and development level have significant impacts on the relaxation variable of the investment index; the cold chain logistics efficiency of fresh agricultural products in Central China,East China, North China and South China is higher than the national average level, while that in Northeast, Southwest and Northwest China is lower than the national average level; scale efficiency is the main factor restricting the improvement of cold chain logistics efficiency of fresh agricultural products. According to the above results, corresponding countermeasures and suggestions are put forward, which can provide decision-making basis and reference for national or local governments to formulate cold chain logistics industry development policies.