[Objective] Soil aggregates, subjected to the joint impact of soil biological and non-biological factors, play a crucial role in determining soil functions and ecosystem services. Soil microorganisms are one of the most active biological factors that affect the formation of soil aggregates. This study is aimed to explore long-term effects of biochar application on stability of paddy soil aggregates in paddy soil at two locations from abiotic and biological perspectives.[Method] From two long-term field experiments under the wheat-rice rotation system, located in Jurong and Nanjing, separately, 3 and 5 years old in history, and consisting of two treatments each, i.e. CK (Conventional fertilization) and AB (Conventional fertilization + biochar), soil samples were collected after harvesting wheat in the annual rice-wheat rotations for particle size fractionation of soil aggregates using the wet sieve method, and for analysis of contents of organic carbon, total nitrogen and total phosphorus as well as abundance of soil microorganisms (bacteria, fungi, arbuscular mycorrhizal fungi, archaea and actinobacteria) in each fraction of soil aggregates using the quantitative PCR technique.[Result] Treatments AB in the two field experiments were significantly higher in macro aggregate ratio (R_>0.25) and field soil water holding capacity after biochar getting aged in situ, and exhibited increase trends in both mean weight diameter and geometric mean diameter (P>0.05). Soil nutrient contents (SOC, total phosphorus) and soil microbial abundance in soil aggregates changed significantly, too. Compared with Treatment CK, Treatment AB was 93.0% and 61.5% higher in content of macro aggregates, respectively, in the Jurong and Nanjing experiments, but exhibited a decreasing trend in both the 0.002-0.053 mm and <0.002 mm fractions of soil aggregates; besides, Treatment AB was significantly or 26.3% and 26.9% higher in SOC content of the bulk soil, 72.4% and 52.3% higher in SOC content of the macro aggregates, and 20.8% and 30.0% higher in SOC content of the micro aggregates, respectively, in the Jurong and Nanjing experiments, significantly higher in fungi abundance of the bulk soil in both experiments, significantly or 25.4% higher in total phosphorus in the Nanjing experiment; and also exhibited an increasing trend in abundance of the arbuscular mycorrhizal fungi and archaea(P>0.05). Correlation analysis showed that the soil aggregate mean weight diameter was very significantly and positively related to macro aggregate ratio, SOC content, abundance of fungi and arbuscular mycorrhizal fungi(P<0.01). The total phosphorus content and archaea abundance were significantly and positively correlated, with correlation coefficient being 0.641 and 0.646, respectively.[Conclusion] Aging biochar improves soil pH, field water holding capacity, other physical and chemical properties, increases the proportion of 0.25-2 mm macro aggregates, SOC and total phosphorus content, and stabilizes soil aggregates. Moreover, it increases abundance of the soil microbes in the rice fields in Jurong and Nanjing to a varying degree. Aging biochar is beneficial to the growth of soil microorganisms, increases the abundance of fungi and arbuscular mycorrhizal fungi, promotes the formation of soil aggregates, and indirectly improves the stability of soil aggregates. To sum up, biochar demonstrates sustained effects of increasing macro aggregate ratio, carbon and phosphorus contents, and fungal, arbuscular mycorrhizal fungal and archaeal abundances, and improving soil aggregate stability during the wheat season of the rice-wheat rotation system.