Greenhouse gas (GHG) production and emission from paddy soils impacts global climate change. Soil particle size fractions (PSFs) of different sizes act as soil microhabitats for different kinds of microbial biota with varying conditions of redox reactions and soil organic matter (SOC) substrates. It is crucial to understand the distribution of soil microbial community structure within PSFs and linkage to the GHG production from paddy soils of China. The change of bacterial and methangenic archaeal community and activity relating to CH(4) and CO(2) production with PSFs under different fertilizer applications was studied in this paper. The fertilization trial was initiated in a paddy soil from the Tai Lake region, Jiangsu, China with four treatments of non-fertilized (NF), fertilized with inorganic fertilizers only (CF), inorganic with pig manure (CFM) and inorganic with straw return (CFS), respectively since 1987, and the PSFs (<2 microm, 2-20 microm, 20-200 microm, and 200-2000 microm) were separated by a low energy sonication dispersion procedure from undisturbed samples. Analysis of bacterial community within different size particles was conducted by PCR-DGGE. The results indicated significant variation of bacterial community structure within different PSFs. The methane was predominantly produced in the coarser fractions, while more species and higher diversity of bacteria survived in the size of <2 microm fractions, in which the bacterial community structure was more significantly affected by fertilizer application practices than in the other coarser fractions. Higher bacterial species richness and more diversities in the smallest size fractions was due to the vicinity between microbes, access to carbon resource outside the microaggregates, and smaller pore size as protective agent suitable habitats for microbes rather than high SOC. Whereas, higher CO(2), CH(4) production and methanogenic archaeal community in coarser fractions may be contributed to storage of labile organic carbon in these fractions. It indicated that availability of SOC in PSFs is mainly factor affected survival of methanogenic archaeal community structure, whereas, bacterium community habitation more affected by physical protection of their location in PSFs. Their activity greatly depended on liability of SOC access to PSFs. Fertilizer application caused more change of bacteria community in clay fraction and greatly increased bacterium and methanogen activity in coarser fractions but only a slight effect on methanogenic archaeal community in the particle size fractions.