The work aims to investigate and analyze the contaminated microorganism of dried fruit of Chinese wolfberry, in order to provide reference for the product quality evaluation standards of dried fruit of Chinese wolfberry in Xinjiang. It was investigated according to the methods in GB 4789—2016 Food Hygiene Microbiology Test Standard and preliminary sterilization application research was carried out. The total number of mold and yeast colonies was 8.9×105 CFU/g, the total number of bacteria colonies was 3.5×105 CFU/g, and the number of coliforms was 1100 MPN among the contaminated microorganisms in the dried fruits of Chinese wolfberry in bulk. Among the contaminated microorganisms of bagged dried Chinese wolfberry, the total number of mold and yeast colonies was 520 CFU/g, the total number of bacteria colonies was 11,000 CFU/g, and the number of coliforms was 150 MPN. The main contaminated molds were Aspergillus niger and Penicillium. After UV irradiation for 10 min, the antibacterial rate of mold and yeast reached 32.44%, and the antibacterial rate of bacteria reached 74.69%. After ultrasonic treatment for 5 min, the antibacterial effect on the total number of colonies was extremely significant, and the antibacterial rate reached 98.21%. Ultraviolet irradiation and ultrasonic treatment can kill the microorganisms on the surface of dried fruit of Chinese wolfberry, and the sterilization effect is good.