Excessive use of chemical fertilizer, unbalanced application of nitrogen, phosphorus and potassium, usually lead to lower utilization of soil fertilizer, decline in the quality of the ecological environment, serious pests and diseases, decrease yield and quality of vegetables. Soil microbiological characteristic is an important characterization of soil quality and can reflect the soil fertility condition. To investigate the effect of fertilizer on soil microorganism, tomato (Lycopersicon esculentum L. Liaoyuanduoli) was used as material, an experimental vegetable field which had 20 years of cultivation history and had been under long-term localized fertilization was used as a platform to analyse the soil microbiological characteristics after different fertilization treatments using PCR-DGGE technology. The results showed that the organic fertilizer application could improve the soil microbial quantity, increase the number of dominant species, increase the dominant population number, stable community structure. Excessive use of nitrogen fertilizer could change the species of soil bacteria dominant populations. Different kinds of chemical fertilizer or fertilizer combinations had no effects on soil microorganism community structure.