The health level of paddy soil is one of the key factors constraining the sustainable increase in rice yield. Four treatments were set up in the experiment: conventional fertilization (T0), milk vetch returning (T1), straw returning (T2), and straw returning combined with organic fertilizer application (T3). The aim was to explore the effects of soil health cultivation measures, such as straw, Chinese milk vetch returning and organic fertilizer application on rice yield, soil physical and chemical properties and health index. The results showed that, compared with conventional fertilization (T0), implementing soil health cultivation measures significantly improved soil physical properties and nutrient level. Specifically, there was a significant decrease in soil bulk density and a significant increase in the proportion of large water-stable aggregates, and the contents of soil organic matter, total nitrogen, available phosphorus, and available potassium all increased significantly. In terms of biological activity, soil health cultivation measures increased soil microbial biomass carbon content, promoted soil respiration, and improved soil microbial diversity index. In terms of rice yield, the rice yield of T3 treatment was 5.1% significantly higher than that of T0 treatment. Although the rice yield of T1 and T2 treatments was lower than that of T0 treatment, but the difference was not significant. The results of soil health assessment using the full data set method showed that soil health cultivation measures could improve the soil health index of paddy field. Among them, the rice paddy soil health index of T3 treatment was the highest, reaching 0.80. In summary, adopting the aforementioned soil health cultivation measures can not only improve the structure of rice paddy soil while ensuring stable rice yields but also enhance soil fertility, biological activity, and health index, thereby promoting the sustainable development of rice production.