Taking a long-term fertilized paddy soil in Taihu Lake region as research object, the enzyme activities in <2, 2-20, 20-200, and 200-2000 microm aggregates under no fertilization (NF), chemical fertilization (CF), chemical fertilization plus straw return (CFS), and chemical fertilization plus pig manure (CFM) were investigated. Fertilization promoted the formation of 200-2000 microm aggregates significantly. The enzyme activities differed with aggregates' particle-size. Urease and invertase activities were the highest in <2 microm aggregates, whereas the activities of cellulase, polyphenoloxidase and FDA hydrolase were the highest in 200-2000 microm aggregates. Fertilization, especially the combined fertilization of inorganic and organic fertilizers, increased the activities of urease, invertase, cellulase and FDA hydrolase in 200-2000 microm aggregates significantly. With the geometric mean (GMea) of the five test enzyme activities as the integrative index of soil enzyme activities, it was found that under fertilization, the GMea was significantly higher in 200-2000 microm aggregates, suggesting the high sensitivity of enzyme activities in larger particle-size aggregates to fertilization practices. Long-term inorganic plus organic fertilization could enhance the soil bio-function via the promotion of the formation of larger particle-size aggregates and the enzyme activities in these aggregates.