In order to explore the effects of nitrogen reduction combined with application of bio-organic fertilizer on rice yield，soil structure and soil carbon sequestration capacity，four treatments were set up，including no nitrogen fertilizer(CK)，conventional fertilizer(T1)，10% nitrogen reduction combined with application of bio-organic fertilizer(T2) and 20% nitrogen reduction combined with application of bio-organic fertilizer(T3).The results showed that，compared with T1 treatment，nitrogen reduction combined with application of bio-organic fertilizer treatments(T2 and T3) had no effect on the rice yield and rice quality，however，significantly increased soil organic matter content and rice nitrogen use efficiency.Compared with T1 treatment，nitrogen reduction combined with application of bio-organic fertilizer treatments(T2 and T3) significantly increased the proportion of soil aggregates of ≥0.25 nm(large aggregates)，decreased the proportion of soil aggregates of <0.25 nm(small aggregates)，and significantly increased the organic matter content in each particle sizes of aggregates.At the same time，T2 and T3 treatments significantly increased the content and proportion of particulate organic carbon in the soil，increased the content of mineral bound organic carbon，however，decreased its proportion in the soil.T2 and T3 treatments simultaneously increased the activities of urease and sucrase，microbial biomass carbon and nitrogen content and the abundance of bacteria and carbon fixing bacteria in the soil.Therefore，in rice production，the application of bio-organic fertilizers could be used to reduce nitrogen fertilizer application，maintain rice yield and maintain soil fertility levels.