[Objective] The effects of single amendment application and combined application of organic fertilizer with amendments on the distribution characteristics of soil aggregates and rice yield of acidic paddy soil were analyzed, in order to provide a scientific basis for the amelioration of acidic paddy soil and the improvement of rice yield. [Methods] Acidic paddy soil was selected as the research object. Seven treatments were set up: control (CK); calcium magnesium phosphate fertilizer (T1), calcium carbonate powder (T2), calcium magnesium silicate conditioner (T3), organic fertilizer+calcium magnesium phosphate fertilizer (T4), organic fertilizer+calcium carbonate powder (T5), and organic fertilizer+calcium magnesium silicate conditioner (T6). The soil aggregate distribution characteristics, aggregate stability, and rice yield under different treatments were compared. [Results] ① Overall, the soil pH value and soil nutrient indicators of T1—T6 showed an increasing trend compared with CK, but not reaching statistical significance. Among them, T5 showed the highest pH value at 4.8, an increase of 0.4 units over CK. Additionally, T1 recorded the highest available phosphorus content at 9.74 mg/kg, representing a 152% increase compared to CK. ② The content of >5 mm aggregates in air-dried soil aggregates of T1—T6 was significantly higher than in CK, with T5 treatment showing the most pronounced effect, an increase of 6.37% compared to CK. ③ The mean weight diameter (MWD), geometric mean diameter (GMD), and >0.25 mm aggregate content (R0.25) of air-dried and water-stable aggregates in T4—T6 were significantly higher than in CK, increasing by 7.51%—8.61%, 26.0%—28.6%, and 6.29%—6.50%, respectively. And the fractal dimension D significantly decreased. ④Rice yield under T1—T6 treatments was significantly higher than that of CK, with the T5 treatment showing the highest increase of 17.46%. [Conclusion] The combined application of organic fertilizer with calcium magnesium phosphate fertilizer, calcium carbonate powder, and calcium magnesium silicate conditioner significantly improves soil structural stability and rice yield, with the organic fertilizer+calcium carbonate powder treatment (T5) demonstrating the optimal effect.