The challenge of reducing the environmental contamination related to agricultural practices to improve nitrogen (N) use efficiency (NUE), carbon (C) sequestration, and crop yield, requires efficient N fertilization and management strategies. We carried out a field experiment from 2016 to 2018 exploring the effect of the gradual replacement of mineral N with organic manure N on soil properties, soil organic C storage, soil total N storage, rice grain yield and yield components, N uptake and C accumulation of rice, and NUE. Moreover, we explained the relationship among the proportions of manure added to fertilizers, soil properties, rice grain yield and yield components, and aboveground N uptake and C accumulation of rice after harvest. Compared to mineral fertilization, 50% manure improved NUE and increased the effective panicle, seed setting rate, grain yield, and straw yield. However, in comparison to mineral fertilization, 100% manure decreased the effective panicle, the number of spikelets per panicle, grain yield, and straw yield and decreased partial factor productivity (PFP), N agronomic efficiency (AEN), and N recovery efficiency (REN). Moreover, in comparison with mineral fertilization, 50% manure increased the aboveground N uptake and C accumulation of rice, decreased the N surplus by 61.5%, and increased the apparent accumulated N recovery efficiency by 10.7%. In comparison to mineral fertilization, manure percentages exceeding 25% increased the total and available N, phosphorus, potassium, and organic C contents in soil. According to redundancy analysis, aboveground C accumulation and N uptake of rice jointly contributed to the variation in grain yields and yield components by 27.9%. In conclusion, 50% manure is a promising ecologically friendly strategy that improves the grain yield, N uptake, C sequestration, and NUE of rice and improves soil fertility. Simultaneously, 50% manure decreases the risk of environmental contamination. © 2022