Abstract Soil microbiology is a key factor in soil organic matter decomposition, and nutrient turnover and availability in agricultural soils, which can be markedly influenced by management practices, such as placement of crop residues, tillage and crop rotation. The present field study was designed as long-term experiment in an experimental farm located in the suburb of Shanghai, China, to study the effects of agricultural management practices on community composition of soil fungi and soil structure. Treatments included burning (crop residues burnt vs . not burnt), tillage (tillage vs . no-tillage) and crop rotation (wheat–corn vs . wheat–soybean). The experiment started in June 2001 and soil samples were collected in March, July and November 2003, i.e. 2 years after establishment. Abundance, diversity and species composition of fungi and soil aggregate composition were analyzed. Hypothesis 1 was that abundance, species richness and diversity of soil fungi would increase in treatments with no-tillage, crop residue retention and wheat–legume rotation compared to tillage, burning and wheat–corn rotation, and Hypothesis 2 that size-distribution of stable aggregates would increase with the diversity of soil fungi. A total of 27 species of fungi of 15 genera were isolated. As the Hypothesis 1, overall soil fungal species richness (6.3 ± 0.4), diversity (2.2 ± 0.1) and total species number (26) in no-tillage significantly exceeded the species richness (4.4 ± 0.3), diversity (1.7 ± 0.1) and total species number (21) in tillage treatments, respectively. However, the effects of tillage depended on soil depth and were most pronounced deeper in soil (10–15 cm soil depth). The Hypothesis 2 was supported by the results: The content of large macro-aggregates (>2000 μm) (295 ± 94 g/kg soil) in no-tillage treatments significantly exceeded that (99 ± 25 g/kg soil) in tillage treatments in 10–15 cm but not in 0–5 cm soil depth, and coincidentally, soil fungal species richness (6.3 ± 0.5) and diversity (2.3 ± 0.1) in 10–15 and also the species richness (6.5 ± 0.5) and diversity (2.3 ± 0.1) in 5–10 cm in no-tillage treatments significantly exceeded the species richness (4.2 ± 0.7) and diversity (1.6 ± 0.3) in 10–15 cm and the species richness (4.3 ± 0.4) and diversity (1.7 ± 0.2) in 5–10 cm in tillage treatments, respectively, but the differences were also not in 0–5 cm soil depth. The results suggest that no-tillage favours fungi and that a more diverse fungal community beneficially affects the formation of large soil macro-aggregates. Further, the results indicate that species richness and diversity of cultivable fungi are useful and distinctive parameters reflecting the status and functioning of the soil fungal community.