Background In soil ecosystems, bacteria and fungi always co-exist in the same niche and interact with each other, especially in different sized soil aggregates. The bacterial and fungal community assembly process and bacteria-fungi interactions in soil aggregates, which is important for bacterial and fungal community diversity and composition, is still unclear.Methods We examined bacterial and fungal community assembly in soil macroaggregate (> 0.25 mm), microaggregate (0.053–0.25 mm) and smaller microaggregate (silt + clay, < 0.053 mm) in an apple orchard. The microbial community assembly processes were analyzed by normalized stochasticity ratio index (NST).Results Bacterial community diversity, composition and assembly were more affected by agricultural practice and aggregate than fungal community. Bacterial community assembly was more stochastic in silt + clay than in macroaggregate, and was more stochastic (NST > 50%) than fungal community in soil aggregates. Meanwhile, bacterial NST was negatively correlated with fungal diversity, and fungal NST was positively correlated with fungal diversity. Co-occurrence network suggested that the bacteria and fungi were less strongly interacting in the network of silt + clay, compared to macroaggregate. The results indicated that fungi impact on the bacterial community assembly in soil aggregate, and the stochasticity of bacterial community assembly was increased with the decrease of interaction between bacteria and fungi in soil aggregates.Conclusions This study enhances our understanding of the mechanism of bacterial and fungal community assembly and co-exists pattern of bacteria and fungi in soil aggregates.