The work aims to improve the design of logistics cold chain disinfection equipment to improve the man-machine comfort and work efficiency in operation of cold chain disinfection equipment, to solve the slow work efficiency of the parcel disinfection chain in the logistics industry, and strengthen the epidemic prevention and control. Based on the ergonomics theory, the principle and structure of the existing logistics cold chain disinfection equipment were analyzed, and the functional layout and structural dimensions of the disinfection equipment were optimized. Jack virtual simulation software was used to compare the cold chain disinfection equipment before and after improvement, and ergonomic simulation verification and evaluation were carried out. Through the simulation, it was concluded that the improved disinfection equipment scheme enhanced the comfort of human body in different work processes, effectively improved the working fatigue of operators, and effectively improved the efficiency of product use. The improved design of cold chain disinfection equipment can form a harmonious and effective human-computer relationship between disinfection personnel and machines. The research results can provide reference for innovative design of disinfection equipment and effective suggestions for epidemic prevention in the cold chain industry during epidemic prevention and control.