Abstract: Clarifying the effects of combined organic-inorganic fertilization with additional biochar-based fertilizer application on the distribution and stability of soil aggregates can provide a theoretical basis for soil fertility enhancement and structural improvement in rice-wheat rotation systems. This study investigated the impacts of organic-inorganic fertilization and biochar-based fertilizer application on crop yield, soil aggregate distribution characteristics, and stability in rice-wheat rotation soils in the middle and lower reaches of the Yangtze River. A two-factor completely randomized block design was adopted, with the main factor being organic fertilizer application methods: conventional fertilization (CF) and organic-inorganic combined fertilization (OF), and the secondary factor being biochar-based fertilizer application methods: no biochar-based fertilizer (NBF) and biochar-based fertilizer application (BF). Compared with CF, OF significantly increased the content of aggregates >0.25 mm (R0.25), mean weight diameter (MWD), geometric mean diameter (GMD), and water-stable aggregate rate (WSAR) (p<0.05), while reducing the aggregate disruption rate (PAD) and fractal dimension (FD) values of soil aggregates calculated by dry and wet sieving by 11.0%, 2.5%, and 1.4%, respectively (P<0.05). Compared with CF, OF significantly increased the annual average yield of wheat and rice grains by 5.7% and 5.6% (p<0.05), respectively, and significantly enhanced the sustainable yield index (SYI) by 5.5% (p<0.05). Compared with NBF, BF significantly increased R0.25, MWD, GMD, and WSAR (p<0.05), while reducing PAD and FD values by 14.2%, 3.9%, and 1.8%, respectively (p<0.05). BF also significantly increased the annual average yields of wheat and rice grains by 8.8% and 6.1% (p<0.05), respectively, and SYI by 7.8% and 6.1% (p<0.05). The combined application of organic and biochar-based fertilizers (OF-BF) exhibited significant synergistic effects, with higher R0.25, MWD, GMD, WSAR, crop yields, and SYI compared to other treatments. Correlation analysis revealed significant negative correlations between FD and R0.25 or WSAR (p<0.01), and highly significant positive correlations between SYI and R0.25 or WSAR (p<0.01). Therefore, the combined application of organic-inorganic fertilization with biochar-based fertilizer is expected to simultaneously improve soil structure and increase crop yields, promoting green and sustainable utilization of rice-wheat rotation soils in the middle and lower reaches of the Yangtze River.