Abstract: Scholars at home and abroad in recent years have focused on researching ammonia nitrogen pollution migration rules in the vadose zone soil. Column simulation and software simulation were primarily conducted for the study of ammonia nitrogen pollution migration. Biotechnology was widely used in degradation of pollutant in soil, but less applied to the study of pollution migration. This study applied Denaturing Gradient Gel Electrophoresis (DGGE) and the sequence analysis of the V3 Region of 16S rRNA combined with canonical correspondence analysis to characterize the bacteria vertical distribution characteristics and bacterial community structure in the soil from three typical contaminated zones in the North China Plain. According to the analysis of physical and chemical soil properties in polluted areas, there were some dominant individual bacteria in the key pathways of the nitrogen cycle and sulfate metabolism. It is suggested that the bacterial communities are affected by the distributions of ammonia, nitrate and nitrite nitrogen, showing that the community structure information of the dominant population in contaminated soil is an important parameter to study the ammonia nitrogen pollution migration rules.