By using phospholipid fatty acids (PLFA) method, this paper studied the soil microbial community structure in the soybean fields with different chlorimuron-ethyl application history in Weihe district of Heilongjiang Province. In the meantime, the residual amount of chlorimuron-ethyl in soil was determined. There was a very low residual of chlorimuron-ethyl in soil under the conditions of different chlorimuron-ethyl application history. With the increasing year of chlorimuron-ethyl application, the total concentration of soil microbial PLFA and the ratios of fungi/bacteria and Gram negative/Gram positive bacteria decreased, and the microbial stress level increased. Principal component analysis (PCA) showed that long-term application of chlorimuron-ethyl into soybean field changed the soil microbial community structure significantly.