The activities of invertase, protease, urease, acid phosphomonoesterase, dehydrogenase, and catalase in different fractions of waterstable aggregates (WSA) were examined in long-term (26 years) fertilised soils. The long-term application of organic manure (OM) with chemical fertiliser (CF) significantly increased macroaggregate and decreased microaggregate percentages, enhanced the mean weight diameter, and significantly increased soil total carbon (TC) and total nitrogen (TN) contents of WSA in different size fractions. Combined fertilisation with OM and CF also increased invertase, protease, urease, acid phosphomonoesterase, dehydrogenase, and catalase activities of WSA in different size fractions. Enzyme activities were higher in macroaggregates than in microaggregates. The distribution of enzyme activities generally followed the distribution of TC and TN in WSA. The geometric mean of the enzyme activities in different WSA of OM-treated soils was significantly higher than that in soils treated with 100% CF or no fertiliser. The results indicated that the long-term combined application of OM with CF increased the aggregate stability and enzyme activity of different WSA sizes, and consequently, improved soil physical structure and increased soil microbial activity. The activities of invertase, protease, urease, acid phosphomonoesterase, dehydrogenase, and catalase in different fractions of waterstable aggregates (WSA) were examined in long-term (26 years) fertilised soils. The long-term application of organic manure (OM) with chemical fertilizers (CF) significantly increased macroaggregate and decreased microaggregate percentages, enhanced the mean weight diameter, and significantly increased soil total carbon (TC) and total nitrogen (TN) contents of WSA in different size fractions. Combined fertilization with OM and CF also increased invertase, protease, urease, and catalase activities of WSA in different size fractions. Enzyme activities were higher in macroaggregates than in microaggregates. The distribution of enzyme activities usually followed the distribution of TC and TN in WSA. The geometric mean of the enzyme activities in different WSA of OM-treated soils was significantly higher than that in so ils treated with 100% CF or no fertilizer. The results indicated that the long-term combined application of OM with CF increased the aggregate stability and enzyme activity of different WSA sizes, and therefore, improved soil physical structure and increased soil microbial activity.