Straw return is an important measure to improve soil organic content and structure on Fluvo-aquic soil. Adding organic fertilizer and microorganism inoculant can stimulate soil biological activity, promote straw decomposition and improve soil enzyme activity. A field experiment on the effects of straw returning via application of organic fertilizer and microorganism inoculant on Fluvo-aquic soil enzyme activities in soil aggregates was conducted. The results showed that: 1) During the entire wheat growing period, compared with onetime and routine fertilization methods, the treatments with organic fertilizer significantly increased the activities of urease, cellulose, invertase and alkaline phosphatase in different size aggregates by 8.15%-66.93%. The treatments with organic fertilizer significantly increased the activities of cellulose and alkaline phosphatase in 0.25–0.053 mm aggregates. 2) Microorganism inoculant addition had increasing effect on the activities of urease, cellulose, invertase and alkaline phosphatase in different size aggregates, but there were differences in the increases of enzyme activities. 3) The enzymes differed in different size aggregates in response to different treatments at different growth stages. Invertase and alakaline phosphatase tended to be lower in seedling stage, peaked at the elongation stage and then decreased at the seedling and booting stages, while urease and cellulose increased steadily throughout the whole growth period. 4) The enzymes differed in different size aggregates in response to different nitrogen fertilizer base/chase ratios, comparatively, the ratio of 5:5 had higher enzyme activities (urease, cellulose, invertase and alkaline phosphatase) than the ratio of 6:4.