A field experiment was carried out to reveal the possibility and mechanism of partially replacing nitrogen fertilizer with organic fertilizer to increase crop yield and improve soil quality, in which, Nanneng 9108 of the rice variety was selected for test, and four treatments were set up (T1, conventional fertilization; T2 and T3, low and high amount of self-prepared organic fertilizer replacing part of conventional nitrogen fertilization; and CK, no fertilization). The results showed that compared with T1, T2 and T3 significantly reduced soil pH, increased the contents of soil organic matter, alkali-hydrolyzed nitrogen, available phosphorus and available potassium, enhanced the activities of urease and alkaline phosphatase, significantly increased rice dry matter accumulation, and increased grain number per spike, seed setting rate, 1000-grain weight and yield during harvest to some extent. In conclusion, organic fertilizer can partially replace conventional nitrogen fertilizer to improve soil quality and increase rice production.