Soil microbial community which indicates soil quality changes and controls the soil ecosystem functions has been regarded as the early warning and the sensitive indicator of soil ecosystem. In order to study the effects of long-term fertilization (1987-2004) on soil microbial community structures, active microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) in the long-term located experiment with different fertilization treatments on brown earth in Shengyang Agricultural University. The results showed that total soil microbial biomass, bacterial biomass and fungal biomass were enhanced significantly with long-term fertilization treatments, especially in manure or manure with chemical fertilizers′ teatments. Fungal biomass in all fertilization treatments decreased during corn heading stage. Soil microbial community structure had been changed due to long-term fertilization, but no predominant group in single nitrogen applied treatment. The microorganisms containing the PLFA of a15:0, i15:0, cy17:0, i16:0, 16:1w7t，10Me18：0 and 15：0 were dominance in microbial community in the treatments applied with manure. In addition, soil organic matter, alkali-hydrolyzable-N, available potassium and available phosphorus were main factors of energy and nutrition for growth and activities of microorganism.