Rice (Oryza sativa L.)–fallow and rice–green manure rotation are two common ecological rotation modes in the Lower reaches of the Yangtze River Basin. In this study, based on a long‐term positioning field experiment, soil microbial community structure (bacteria and fungi) and physicochemical properties were investigated and compared to comprehensively evaluate the effects of rice–fallow (RF) and rice–bean (Vicia faba L.) (green manure, RB) rotation on soil health, thus providing scientific basis for the utilization mode of paddy field in winter. The results showed that (a) compared with RF, the contents of soil organic matter (SOM), humic acid (HA), total N, and soil alkaline phosphatase in RB were significantly enhanced by 33.84, 71.04, 35.48, and 54.38%, respectively (p < .01); available K content in RF was increased by 22.84% compared with RB (p < .01); (b) the soil macroaggregates with a diameter more than 0.25 mm (R0.25), mean weight diameter, and geometric mean diameter (GMD) in RB treatment were significantly higher than those of RF by 112.67, 60.25, and 64.88%, respectively (p < .05); (c) different rotations altered bacterial community structure significantly, but exhibited less effect on that of fungi; bulk density, pH, GMD, SOM, and HA were the key environmental factors shaping the bacterial and fungal community structure. The alteration of specific bacterial and fungal taxa revealed that RB had a more promising potential to promote crop growth and improve organic matter decomposition. Therefore, rice–green manure rotation demonstrated a stronger positive effect on soil physicochemical and microbial properties.