Soil aggregation, microbial community, and functions (i.e., extracellular enzyme activities; EEAs) are critical factors affecting soil C dynamics and nutrient cycling.  We assessed soil aggregate distribution, stability, nutrients, and microbial characteristics within >2, 0.25–2, 0.053–0.25, and <0.053 mm aggregates, based on an eight-year field experiment in a greenhouse vegetable field in China.  The field experiment includes four treatments: 100% N fertilizer (CF), 50% substitution of N fertilizer with manure (M), straw (S), and manure plus straw (MS).  The amounts of nutrient (N, P₂O₅, and K₂O) input were equal in each treatment.  Results showed higher values of mean weight diameter in organic-amended soils (M, MS, and S, 2.43–2.97) vs. CF-amended soils (1.99).  Relative to CF treatment, organic amendments had positive effects on nutrient (i.e., available N, P, and soil organic C (SOC)) conditions, microbial (e.g., bacterial and fungal) growth, and EEAs in the >0.053 mm aggregates, but not in the <0.053 mm aggregates.  The 0.25–0.053 mm aggregates exhibited better nutrient conditions and hydrolytic activity, while the <0.053 mm aggregates had poor nutrient conditions and higher oxidative activity among aggregates, per SOC, available N, available P, and a series of enzyme activities.  These results indicated that the 0.25–0.053 mm (<0.053 mm) aggregates provide suitable microhabitats for hydrolytic (oxidative) activity.  Interestingly, we found that hydrolytic and oxidative activities were mainly impacted by fertilization (58.5%, P<0.01) and aggregate fractions (50.5%, P<0.01), respectively.  The hydrolytic and oxidative activities were significantly (P<0.01) associated with nutrients (SOC and available N) and pH, electrical conductivity, respectively.  Furthermore, SOC, available N, and available P closely (P<0.05) affected microbial communities within >0.25, 0.25–0.053, and <0.053 mm aggregates, respectively.  These findings provide several insights into microbial characteristics within aggregates under different fertilization modes in the greenhouse vegetable production system in China.