To investigate the long-term effects of combined organic and inorganic fertilizer application on the structural stability and fertility of soil in paddy fields located in the cool northeastern region of China, a long-term fixed-site experiment was initiated in 2017. The experiments included the following five treatments: 100% conventional chemical fertilizer NPK (CK), conventional PK fertilizer without N fertilizer (T1), 30% organic N and 70% chemical N fertilizers with conventional PK fertilizer (T2), 50% organic N and 50% chemical N fertilizers with conventional PK fertilizer (T3), and 100% organic N fertilizer (T4). Notably, the total amount of fertilizer applied remained consistent across treatment groups. The results revealed that the combination of organic and inorganic fertilizers significantly increased rice yields and nitrogen use efficiency, with the T3 treatment performing the best. Compared with CK, T3 resulted in a 24.26% greater rice yield, and it increased the nitrogen agronomic efficiency by 71.05%. There were no significant differences among the treatment groups in terms of the proportions of soil aggregates larger than 2 mm or smaller than 0.053 mm. Nitrogen fertilizer application reduced the proportion of 0.053–0.25 mm aggregates and promoted the formation of predominantly 0.25–2 mm aggregates. However, the different organic–inorganic combinations did not cause significant differences in soil aggregate structure or stability. Compared with the CK treatment, the application of both organic and inorganic fertilizers increased soil organic matter content, decreased N₂O emissions, and increased soil catalase activity. In summary, the application of 50% organic N and 50% chemical N fertilizers with conventional PK fertilizer (T3) was determined to be the optimal combination for achieving high and stable rice yields in the cool northeastern region of China while increasing the structural stability and fertility of the soil.