Taking a long-term fertilized paddy soil in Taihu Lake region as research object and continuously rice-rape rotation has been conducted. The microbial community structures and diversity in < 2, 2-20, 20-200, and 200-2 000 μm aggregates under no fertilization (NF), chemical fertilization (CF), chemical fertilization plus straw return (CFS) were investigated through by PCR-DGGE analyze. The results showed that fertilization, chemical fertilization plus straw return, affected the bacteria and fungi community structures in 2 000-200 μm and 200-20 μm aggregates more than chemical fertilization only, which suggested the high sensitivity of microbial community structure changes in the larger aggregates. There were significant difference of microbial community structure diversity in different aggregates, the diversities in 2 000-200 μm and＜2 μm aggregates were higher for bacteria and higher in larger aggregates for fungi. The variance caused by different aggregates was more than different fertilization.