Abstract: Clarifying the effects of organic substitution, biochar or biochar-based fertilizer application on the simultaneous improvement of paddy soil quality and rice grain yield, can provide a theoretical basis for the sustainable utilization of paddy field in the middle and lower reaches of the Yangtze River in China. Pot experiments were conducted to explore the effects of biochar or biochar-based fertilizers application under organic substitution on soil quality, rice growth and nitrogen use efficiency. This study included the following eight treatments: control (CK), conventional fertilization (CF), biochar addition (BC), organic substitution (OF), biochar-based fertilizer addition (BF), conventional fertilization with biochar (CF+BC), organic substitution with biochar (OF+BC), and organic substitution with biochar-based fertilizer (OF+BF). The results revealed that compared with the CK, the pH values significantly increased by 0.22, 0.13, 0.26 and 0.18 units in BC, BF, OF+BC and OF+BF, respectively. The soil organic carbon contents significantly increased by 8.8%~17.8% in the treatments with organic fertilizer, biochar or biochar-based fertilizer application and the total nitrogen contents significantly increased by 9.3%~12.7% in the treatments with organic fertilizer or chemical fertilizer application relative to the CK, with the OF+BC showing the largest increase. Compared with the CK, the contents of available phosphorus, available potassium and microbial biomass carbon (MBC) in the other treatments significantly increased by 14.3%~5.9%, 5.5%~19.9% and 14.2% ~54.0%, respectively, and the ammonium nitrogen content in OF, CF+BC, OF+BC and OF+BF could also significantly increased by 24.8%~41.5%, with the OF+BC showing the largest increase. The trends of soil urease, sucrase, alkaline phosphatase, acid phosphatase and catalase activities among treatments were similar to the MBC, and there was no significant difference between OF+BC and OF+BF. Compared with the CK, the soil quality index, rice grain yield and the ccumulation of nitrogen, phosphorus and potassium in the other treatments could significantly increased by 78.3%~209.1%, 27.3%~93.0%, 30.2%~117.3%, 32.6%~101.9% and 37.1%~104.0%, respectively, with the OF+BC treatment showing the largest increase. Meanwhile, the nitrogen recovery rate significantly increased by 27.4%, 55.3%, 83.1% and 72.0%, in BF, CF+BC, OF+BC and OF+BF, respectively, relative to the CF. Therefore, the application of biochar or biochar-based fertilizer under organic substitution can promote the simultaneous improvement of soil quality and rice grain yields, which is beneficial to the sustainable utilization of paddy fields in the middle and lower reaches of the Yangtze River in China.