Abstract: Objective This study aims to investigate the effects of temporary depuration on the body composition, oxidative stress, the structure and function of bacterial communities of Crassostrea hongkongensis. Methods This study carried out a 96-hour depuration treatment on shelled C. hongkongensis. Subsequently, the changes of survival rate, body composition, and oxidative stress enzyme activities were analyzed during depuration. 16S rRNA sequencing was employed to analyze the structure and functions of microbial community. Results The results indicated that the crude protein content of C. hongkongensis exhibited significant fluctuations during depuration. Meanwhile, the crude fat content remained at a relatively high level, and the ash content decreased. During depuration, the superoxide dismutase (SOD) activity reached its peak (442 U/g) at 24 h, whereas the catalase (CAT) activity reached minimum value (55 μmol/min/g) at 72 h, the glutathione peroxidase (GSH-Px) activity and malondialdehyde (MDA) content reached their maximum values (167 μmol/min/g, 242 nmol/g) at 96 h. The analysis of microbial community demonstrated that the depuration time had a significant influence on the microbial community structure of C. hongkongensis, and 48 h was the critical time point for the change in microbial community structure. Proteobacteria and Bacteroidetes were the dominant phyla, accounting for over 85% of the total bacterial abundance. The KEGG signaling pathway enrichment results revealed that the functions of bacterial-mediated environmental adaptation, immune system, protein folding, sorting and degradation, and nucleotide metabolism were significantly higher in C. hongkongensis during 24-72 h compared to 0 h and 96 h. Conclusion Based on the above findings, the appropriate depuration duration for C. hongkongensis was 48-72 h. This result offers a scientific reference for the enhancement of C. hongkongensis quality.