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[Objectives] The aim was to explore the biological mechanism of green manure on improving soil fertility in paddy soil. [Methods] Early rice (chemical fertilizer) was used as a control to study the effects of returning green manure crops of mung bean, lablab bean to paddy fields and organic manure application on the bulk density, nutrient content, nutrient content and yield of rice soil. [Results] The soil bulk density in each treatment was significantly lower than that of the basic soil. The soil bulk density of treatment I was the least of 1.52 g/cm³. The nitrogen content of rice in treatment IV was significantly higher than that of treatment I, treatment II, and treatment III. The phosphorus and potassium contents of rice in treatment III and treatment IV were significantly higher than those of treatment I and treatment II. Returning green manure crops to field and applying organic fertilizers could increase the polished rice ratio and reduce the chalkiness degree, chalkiness ratio and protein content of rice. The gel consistency of rice grain in treatment I was significantly higher than that of treatment II, treatment III and treatment IV. The rice of treatment III had the highest number of effective panicles per plant, 1 000-grain weight, theoretical yield and actual yield, respectively, 14.07 panicles/plant, 32.58 g, 6 236.27 kg/hm² and 5 086.80 kg/hm². [Conclusions] This study provided a theoretical basis for proposing good green manure varieties suitable for the continuous improvement of paddy soil quality. [ABSTRACT FROM AUTHOR]