Excessive reliance on chemical fertilizer (CF) in conventional farming is a serious concern owing to its negative effects on soil health, the environment, and crop productivity. Organic manure is an alternative source of fertilizer to reduce the amount of CF usage in agriculture, decrease environmental pollution, and ensure sustainable crop production. This study assessed the integrated effect of poultry manure (PM) and cattle manure (CM) with CF on soil properties, plant physiology, and rice grain yield. Additionally, the difference in pre-and post-anthesis dry matter (DM) and nitrogen (N) accumulation and their relationship with grain yield was also determined. Pot experiments were performed in the early and late growing season at the experimental station of Guangxi University, China, in 2018. A total of six treatments, i.e., T 1-CF 0 ; T 2 −100% CF; T 3 −60% CM + 40% CF; T 4 −30% CM + 70% CF; T 5 −60% PM + 40% CF, and T 6 −30% PM + 70% CF were used in this pot experiment. Results showed that T 6 enhanced leaf photosynthetic efficiency by 11% and 16%, chlorophyll content by 8% and 11%, panicle number by 12% and 16%, and grain yield by 11% and 15% in the early and late seasons, respectively, compared to T 2. Similarly1, post-anthesis N and DM accumulation, N uptake, and soil properties (i.e., soil organic carbon, total N, and bulk density) were improved with integrated CF and manure treatments over the sole CF treatments. Interestingly, increases in post-anthesis N uptake and DM production were further supported by enhanced N-metabolizing enzyme activities (i.e., nitrate reductase, glutamine synthetase, and glutamate oxoglutarate aminotransferase during the grain-filling period in combined treatments. In-addition, the linear regression analysis showed that postanthesis DM (R 2 = 0.95) and N (R 2 = 0.96) accumulation were highly associated with grain yield of rice. Thus, the combination of 30% N from PM or CM with 70% N from CF (i.e., urea) is a promising option for improvement of soil quality and rice grain yield. Furthermore, our study provides a sustainable nutrient management plan to increase rice yield with high N use efficiency.