Objective To understand the composition of microbiota on the surface of fresh eggshell and its change over time. Methods The samples were collected from three cities and tested at different time points. The diversity and similarity of bacteria were analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and sequencing method. Results The Shannon index and Dice index of bacteria on eggshell surface of Hanzhong were statistically significant different from Yulin and Xi'an. The bacteria were mainly Firmicutes and Actinobacteria, and the dominant genera were Staphylococus, Streptomyces and Lactobacillus. Conclusion There were different bacteria on the surface of eggshell in different areas, but the microbiota in the early and late stage of storage time was very similar.