Under the background of the rapid development of cold chain logistics industry and the construction of Beibu Gulf Port as an international gateway port and hub port，this paper comprehensively analyzes the significance of the development of cold chain logistics in Guangxi and fully understands the development status of cold chain logistics in Guangxi. Through the DEA model，based on the input-output data index of agricultural cold chain logistics，effectively measure the efficiency of the current agricultural cold chain logistics in Guangxi. The development of cold chain logistics in Guangxi has the following characteristics：the arrival of new development opportunities，logistics system plays an obvious role；port cold chain demand surge；the cold chain foundation in Guangxi is gradually consolidated，and the efficiency of customs clearance is further improved. The three ports cold chain has obvious functional characteristics and a promising prospect for synergistic development. Finally，suggestions are given for the high-quality construction and development of Guangxi port cold chain system：make clear the development orientation and overall layout of Beibu Gulf port cold chain；planning and construction of cold chain logistics infrastructure should be increased；through demand traction to improve the market circulation main organization ability；actively cultivate the main body of cold chain logistics and improve the efficiency of port cold chain logistics through informatization level.