Organic fertilizer plays a critical role in developing sustainable cropping systems due to its positive impacts on soil fertility, crop productivity, and environmental sustainability. Yet, a systematic and quantitative analysis on how organic fertilization affects soil physicochemical properties, nutrient uptake and physiological use efficiency, agronomic characteristics, yield, and yield components of rice (Orzya sativa L.) is lacking. In this study, a synthesized three-level meta-analysis from 74 peer-reviewed papers which concentrated on rice production with organic fertilizer application at 85 sites in subtropical China was conducted to investigate how organic manure affects soil fertility and rice productivity. The results showed that organic fertilization significantly increased soil organic carbon (SOC) by 15.6 %, and available nutrients varied from 2.3%–20.2%. Moreover, organic fertilization significantly increased leaf area index, content of chlorophyll, and total biomass accumulation at grain-filling and ripening stages, which was favorable to the promotion of grain filling. Overall, organic fertilization significantly increased rice yield by 8.3 %, which was attributed to the higher nutrient uptake and physiological use efficiency. In addition, the response of rice yield was various under different subcategories. The magnitude of the increase in rice yield was the greatest under the treatment with animal manure (10.5 %), followed by biochar (8.3 %) and crop straw (7.2 %) due to the higher SOC sequestration and nitrogen use efficiency with animal manure incorporation compared with biochar and crop straw amendment. In addition, organic fertilization was most effective at improving the rice yield when the content of SOC was <10 g kg⁻¹, indicating that it was an effective way to improve the crop production of infertile soil. The response of rice yield to organic fertilization increased as the experimental duration increased, which was of great significance as the rice yield could be improved through long-term application of organic fertilizer. The results of the present study indicated that organic fertilization is an effective practice for rice production in subtropical China.