Background Domestic waste classification is one of the major livelihood projects in China. With the introduction of the Shanghai Household Waste Management Regulation in 2019, the work of domestic waste classification has been carried out nationwide, yet its potential risks especially those derived from microorganisms are not clear. Objective To investigate the microbial characteristics of the domestic waste in typical residential areas in Shanghai, and provide a theoretical basis for health protection during the domestic waste classification process in Shanghai and throughout China. Methods Dry and wet waste from a typical residential community in Shanghai were collected during 2019–2020. Microbial colonies were counted in domestic waste and analyzed for growth patterns. Then through 16S rRNA sequencing using lllumina PE250, hierarchical clustering analysis was conducted to reveal the similarity and dissimilarity of community compositions in different domestic waste groups, alpha diversity was estimated to reflect the richness and diversity of bacterial communities, principal co-ordinates analysis of unweighted UniFrac distance was performed to estimate the beta diversity, and linear discriminant analysis effect size (LEfSe) was used to find features differentially represented among domestic waste groups. Results In the chosen typical residential community of this study, the numbers of microorganisms in waste were quite different, with lower numbers of microorganisms in dry waste than the numbers in wet waste. In addition, different growth curves of microorganisms were shown for different seasons, and the peak baterial colony numbers were 200 CFU·cm⁻², 6×10⁵ CFU·mL⁻¹, 10 CFU·cm⁻², and 2×10⁶ CFU·mL⁻¹ for summer dry waste, summer wet waste, winter dry waste, and winter wet waste, respectively. The results of 16S RNA demonstrated significant differences in α and β diversity indicators among different waste groups, and the difference in waste classifications was larger than the difference of the same classification of waste in different seasons. The main compositions of bacterial colonies in domestic waste was Proteobacteria, followed by Firmicute and Bacteroidota. The clustering analysis showed that the microbial composition in summer dry waste was close to that in winter dry waste, while other groups were quite different. In total 48 differential bacterial taxa were found at the level of genus including Pseudomonas and Pantoea. Conclusion Different seasons and different classifications of domestic waste present varied microbial characteristics, with different potential pathogenic microorganisms. Together with other related studies, we suggest that different measures should be taken for different domestic wastes to prevent and control the health hazards associated with waste classification.