Microorganisms play an important role in plant growth, health and ecological function. It is necessary to explore the microbial community because of the significant ecological and economic value of apples (Malus x domestica). However, the related bacterial communities in different ecological habitats are not clear in the unique scion/rootstock combinations of apples. In this study, the Illumina Miseq platform was used to analyze the bacterial communities in different niches (bulk soil, rhizosphere soil and roots) of two scion/rootstock combinations (Fuji/Malus xiaojinensis Cheng et Jiang (Mx) and Fuji/Malus baccata (L.) Borkh. (Mb)). The relationship between the microbial community, soil properties, and plant characters was explored. The results showed that the diversity of the bacterial community decreased from bulk soil to rhizosphere soil and then to roots. In addition, at the phylum level, Proteobacteria, Actinobacteria and Acitinobacteria were dominant and had notable divergence in different ecological niches. Distinct niches had remarkable effects on the diversity and composition of the bacterial community according to PCoA. The rootstock genotype had an effect on the bacterial composition but no effect on the diversity. pH, soil organic matter (SOM), alkaline hydrolyzable nitrogen (AN) were the main factor affecting the structure of bacterial community in rhizosphere soil, as shown by Pearson analysis. Bacteria taxa in the roots were affected by starch, fructose, sucrose and sorbitol. This study showed the microbial community structure in different ecological niches of different scion/rootstock combinations and provided some evidence for understanding the microbial-plant interaction of apple rootstocks.