Soil samples were collected from soils under different vegetations, i.e. T (tussock), S (shrub), SF (secondary forest) and PF (primary forest), representing different vegetation restoration stages in the Karst region in Southwest Guangxi, China, for analysis of genetic diversity of ammonia-oxidizing bacteria (AOB) and their relationships with urease activity and physico-chemical properties of the soil. Results show that with the advancement in vegetation restoration, genetic diversity and Shannon and Evenness indices of AOB in the soil increased except for under tussock, and moreover, AOB community structure altered, with changes embodied in inconsistent distribution of Nitrosospira clusters 3a and 3b populations as a result of variation of the sensitivity of Nitrosospira cluster 3 population to ammonium concentration. Correlation analysis reveals that soil urease activity in the soil was positively related to ammonium content. Hence, soil urease may alter AOB diversity by affecting ammonium content. However, at the late stage of vegetation restoration, the lower ammonium content did not lead to any reduction in AOB diversity. LIBSHUFF and RDA analysis exposed that AOB community structure was closely related to vegetation type, soil urease activity and soil pH, indicating that vegetation, soil N availability and pH may possibly be the main factors affecting soil AOB diversity. These findings may serve as certain scientific basis for further understanding of soil N cycling in Karst region.