Abstract: 【Objectives】 Yellow clayey paddy field is one of the major middle-low-yielding fields in southern China. Soil microorganism and aggregate composition affect the soil fertility and productivity. Study on the effect of fertilization on them will help understanding the mechanism of building soil fertility through reasonable fertilization. 【Methods】 The 28-years?? long term field fertilizer experiment in Fujian Province was used for the investigation. There were four treatments, CK (without fertilizer), NPK (fertilizer N, P and K), NPKM (NPK plus cattle manure) and NPKS (NPK plus rice straw). The soil samples were collected in the 0-20 cm soil layer, phospholipid fatty acid technique and wet screening method were employed to study the microbial community structure and water-stable aggregate composition, respectively. 【Results】 Compared with CK, the long-term fertilization could increase the types of soil microbial phospholipid fatty acid by 16.67%-38.89% and soil microbial biomass by 26.71%-47.30%,which had significant differences of bacterial, fungi and actinomycetes. The no fertilization could lead to the shortage of actinomycetes, but the fertilization with cattle manure (NPKM) could promote the species and amount of soil microbial. The first and second principal components explained 89.80% of the total variance in soil phospholidid fatty acids which extracted six main variables, C17: 1w8 (Gram-negative bacteria), C12: 0 (bacteria), cy19: 0w8 (Burkholderia), C17: 0 (Arthrobacter), C18: 1w7 (Pseudomonas), and C10Me17: 0 (Actinobacteria). Meanwhile the NPKM and NPKS treatments could increase the ratios of 0.25-2.0 mm water-stable aggregate by 4.74-8.47 percentage points, and the fertilization could increase the contents of C and N in above aggregate by 1.63%-32.58% and 3.82%-13.74%, respectively. The NPKS treatment could promote the formation of water-stable aggregate larger than 0.25 mm. The NPKM treatment could increase the contents of C and N in aggregate with different sizes. There were significantly positive correlations between bacterial, actinomycetes or total microbial biomass and water-stable aggregate of 0.25-2.0 mm size, while there were significantly negative correlations between bacterial, actinomycetes or total microbial biomass and water-stable aggregate less than 0.25 mm. There were significantly positive correlations between bacterial or total microbial biomass and the carbon content in aggregate with different sizes. 【Conclusions】 The fertilization could significantly increase the microbial species and biomass, promote the formation of water-stable aggregate larger than 0.25 mm, and increase the contents of C and N in different-sized aggregate. These findings indicated that the fertilizer with cattle manure (NPKM) was the best fertilizer regime in the yellow clayey paddy field.