The aim of this study is to investigate soil ammonia-oxidizing bacterial community composition, abundance, phylogenetic relationship and diversity under different plant communities formed in the evolution process of eutrophic inland lake Wuliangsuhai, and to discuss the impacts of soil physicochemical factors on ammoniaoxidizing bacterial community structure. The total DNA was extracted and a clone library was constructed based on amoA gene in order to analyze ammoniaoxidizing bacterial community composition, abundance, phylogenetic relationship and diversity index. Soil substrate conditions were analyzed to assess their effects on ammoniaoxidizing bacterial community composition. The similarity of ammoniaoxidizing bacterial community composition gradually decreased from eutrophic lake sediments to desertification soil. The dominant species significantly changed from the Nitrosomonaslike group to the Nitrosospiralike group. Correlation analysis indicated that the combination of total nitrogen and total water soluble salt had the most significant effect on the ammoniaoxidizing bacterial community structure, and the correlation coefficient was 0.943. The diversity index showed that reed swamp and Nitraria tangutorum desert soil were more suitable for diverse ammonia-oxidizing bacteria to grow. Ammonia-oxidizing bacterial diversity and dominant species changed significantly in the transition zone between wetland sediment and desert soil. Total nitrogen and total water soluble salt are the major environmental factors influencing spatial heterogeneity of ammonia oxidizing bacterial community composition.