This study investigated the effects of warming (about 1 °C) on the biomass and composition of microbial communities and enzyme activities in soil macroaggregates and microaggregates. We fractionated the bulk soils from the control and warming treatments into large macroaggregates (>2000 μm), small macroaggregates (250–2000 μm) and microaggregates (<250 μm) using the optimal moist sieving approach. Warming did not significantly affect soil microbial biomass in all aggregate fractions, but significantly altered the soil microbial community composition in the large macroaggregates. The G+:G− ratio was significantly higher in the small macroaggregates and microaggregates than that in the large macroaggregates in warmed soils, while the stress ratio was significantly higher in the large and small macroaggregates than that in the microaggregates. Soil warming did not significantly affect β-glucosidase, cellobiohydrolase and N-acetylglucosaminidase activities, but significantly decreased acid phosphomonoesterase activity and increased oxidase activities. Our results suggest that soil microbial community composition in the large macroaggregates might be more sensitive to warming. The differential responses of soil microbial communities and enzyme activities in different aggregate fractions in the warmed soils may have important implications for C cycling in subtropical forest ecosystems.