This study determined the best pre-treatment approaches for egg sources by comparing the effects of different physical， chemical and physical-chemical coordinated disinfection method on the surface microorganisms of egg sources. The metagenomics technology was used to analyze the optimized disinfection methods before and after eggshell surface treatment population diversity. The results showed that the physical-chemical coordinated disinfection method had the best effect on the microorganisms on the surface of the egg source. By immersing the eggs in a 125 mg/L chlorine dioxide solution for 5 minutes and then rinsing at 65 °C with hot water for 120 s， the sterilization rate of microorganisms on the surface of the eggshell reached 99.9%， which marked best pre-treatment method. The microbial community richness and community diversity on the surface of the egg source after pretreatment were significantly reduced （P<0.05）， with phylum level OTU reduced from 19 to 4， genus level OTU reduced from 258 to 29， and the abundance of Escherichia and Staphylococcus reduced to 0. The method can effectively kill the microorganisms on the surface of the eggshell and provides a good technical guarantee for the preservation and processing of egg products.