Flooding in tea plantations is a common natural event that often has adverse effects on soil production, such as soil quality decline, tea growth inhibition, and tea yield and quality reduction. The aim of the present study was to investigate the impacts of varying flooding durations on soil properties and soil microbial community structure. Plots in a tea plantation were subjected to different durations of flooding (1, 3, 4, 5, 6, and 7 d) to analyze changes in soil physicochemical properties, heavy metal concentrations, and microbial community structure. According to the results, with prolonged flooding, soil pH, and organic matter (OM), available potassium (AK), available phosphorus, and eight heavy metal concentrations increased initially before decreasing. Following flooding, the dominant bacterial phyla were Proteobacteria, Acidobacteriota, Chloroflexi, and Actinobacteriota, whereas the dominant fungal phyla were Ascomycota and Basidiomycota. Additionally, there were significant correlations between soil nutrients and soil microbial community composition, with OM, AK, and pH contributing most significantly to bacterial community composition, and AK followed by OM, chromium, and arsenic contributing most significantly to fungal community composition. The results of the present study provide a theoretical basis for the improvement and management of tea plantation soils under flooding.