To explore the difference of bacterial community structure and diversity of biocrustal horizons and subsoil under different heavy metal pollution levels and the influencing factors, a mining area and an enclosed grassland with wide-spread biocrusts in eastern Ningxia were selected as study area, the algal and moss biocrusts were selected as study objects. High throughput sequencing technique was used to measure the difference of bacterial community structure and diversity of A horizon (biocrustal horizon) and B horizon (subsoil). The relationships between bacterial community structure and diversity and soil environmental factors were explored by the correlation analysis and redundancy analysis. The results indicated that:(1) compared with the enclosed grassland, the two kinds of biocrust in mining area had more significant surface enrichment effect of heavy metals derived from atmospheric dust fall, and demonstrated a significantly interspecific difference as followed Moss crust >Algal crust. Pollution load index indicated that the biocrusts in mining area had a higher pollution level and demonstrated as A horizon had a higher pollution level than B horizon. (2) The dominant bacterial community phylum in the two habitats were basically uniform, and relative abundances of which decreased in the order of Actinobacteria, Proteobacteria and Acidobacteria. Due to the influences of biocrust type and heavy metal pollution level, there were significant difference in bacterial community structure between the two habitats. It mainly demonstrated that the alpha indices in A and B horizons of algal crust were higher than those in the enclosed grassland, while the diversity indices in A and B horizons of moss crust in mining area were higher but the richness indices were lower than those in the enclosed grassland. The principal coordinate analysis indicated that the bacterial community structure of biocrusts in different habitats was differed while in the same habitat was similar. Heavy metal contents of As, Pb, soil clay particles contents, and pH were the main soil environmental factors that influence the bacterial community structure and diversity of biocrusts. Human activity is the main driver of structural variation in bacterial communities.