Abstract: Nitrogen significantly affects the growth and the quality of tobacco, which absorb the most nitrogen fertilizer from the soil. The physical and chemical properties of the soil and the soil microbial will change according to the different amount of nitrogen, which directly affect the growth and development of the tobacco. An experiment with two different levels of nitrogen 131kg/hm2 (model1,the normal level of nitrogen, CK)and 168kg/hm2(model2)respectively, was conducted to examine the effects of different nitrogen fertilizer on soil physical and chemical properties and soil microbial in Yunyan87, which was widely planted in Southwest of China, in Pengshui county of Chongqing, China. On the whole, model2 can improve the physical and chemical properties of the soil, such as improving soil organic matter, available potassium and phosphorus content, but has a low level of available nitrogen. In addition, compared with the mode1, in the 75th day after transplanting, mode2 significantly reduce the soil pH. The improvement of soil properties contribute to increasing the number of bacteria, actinomycetes and fungi.ect, which will be good for decomposition and improving soil quality.