The effects of the long-term application of inorganic fertilizers on microbial community diversity were investigated in a rice-planting soil derived from quaternary red clay in the Ecological Experimental Station of Red Soil, Chinese Academy of Sciences. After 13 years application of different inorganic fertilizers for flooded double rice crops, the community structure of bacteria, archaea, actinomycetes, and fungi in the soil changed greatly. The similarity of the SSU rDNA DGGE patterns of these four kinds of microorganisms between the soil without rice-planting and the soil with rice-planting reached only 33% and 66%, respectively. The microbial community structure among treatments with NP, PK, and NPK types of P fertilizer were much similar; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms in these treatments reached a high range of 75%-81%. The microbial community structures between the treatment with N and K fertilizers (NK) and the treatment without inorganic fertilization (CK) with the treatments with P fertilizer differed greatly, with the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms in these treatments reaching 69%-77% and 55%-77%, respectively. The results of this study provide a scientific basis for fertilizing and utilizing soil, protecting microbial diversity, and accomplishing the sustainable development of agroecology.