Abstract Abundance and allocation of organic matter, microbial community and their extracellular enzyme activities in soil aggregates had been increasingly concerned for mediating biogeochemical cycle and biodiversity provided by soil. In this study, the variations of soil organic carbon (SOC) accumulation and extracellular enzyme activities in aggregate size fractions of a rice paddy with long-term fertilization treatments were analyzed. These treatments included no fertilizer application (NF) as a control, chemical fertilizer only (CF), chemical fertilizer combined with swine manure (CFM), and with straw residue return (CFS). Hereby, size fractions of soil aggregates respectively of >2000 μm (large macroaggregates), 250–2000 μm (macroaggregates), 53–250 μm (microaggregates), 2–53 μm (fine aggregates), and 53 μm. Whereas, activity of phenol oxidase was generally concentrated in soil aggregate fractions in size between 2 and 2000 μm while that of peroxidase in size between 53 and 2000 μm. Activity of β-glucosidase and cellobiohydrolase was both significantly elevated under CFS and that of peroxidase under CF, CFM and CFS treatments, but phenol oxidase activity was suppressed under CFS treatment. The enzyme activities of β-xylosidase, β-glucosidase, cellobiohydrolase and N-acetyl-glucosaminidase varied greatly (CVs up to 50%), rather with size fractions than with treatments, while those of α-Glucosidase and phenol oxidase varied moderately (CVs up to 35%), rather with treatments than with size fractions. However, those of acid phosphatase and peroxidase changed slightly (CVs up to 20%), regardless of both size fractions and fertilization treatments. Thus, abundance and enrichment of all the soil enzyme activities analyzed depended not on SOC although the overall extracellular enzyme activity was generally well correlated to SOC abundance, among aggregate size fractions. Only activities of carbon-degrading enzymes were greatly enriched in macroaggregates, which were seen reduced under combined organo/mineral fertilization. This study highlighted macroaggregates as biochemically active micro- hotspots and lower activities of carbon-degrading enzymes with SOC accumulation under long-term rational fertilization in the rice paddy.