Aims To select apple rootstocks that are tolerant to low nitrogen and reveal the relationship between the rhizosphere bacterial communities and the low nitrogen tolerance of the apple rootstock. Methods and Results In total, 235 lines of hybrids of Malus robusta Rehd. x M.9 with low nitrogen stress were cultivated in pots in a greenhouse equipped with a drip irrigation system, and growth characteristics, photosynthesis traits and mineral elements were monitored. The bacterial community structure of the rhizosphere from different rootstocks was determined via Illumina MiSeq sequencing. This study selected three low nitrogen-tolerant (NT) lines that had higher nitrogen concentration, and higher photosynthesis rate than the three low nitrogen-sensitive (NS) lines. The bacterial community structure significantly differed (P <= 0.001) among the rootstocks. The bacterial phyla Proteobacteria and Actinobacteria were the dominant groups in the rhizosphere and presented higher abundance in the NT rhizosphere. The N concentration in the apple rootstocks exhibited highly positive Pearson correlations with the bacterial genera Sphingomonas, Pseudoxanthomonas, Bacillus and Acinetobacter, and negative correlations with the bacterial genera Pseudarthrobacter and Bradyrhizobium. Conclusions This study showed that investigated rootstocks achieved increased nitrogen concentration by enhancing their photosynthetic production capacity and shaping their rhizobacteria community structure. Significance and Impact of the Study The findings provide a basis for studying the mechanisms of resistance to low nitrogen stress in apple rootstocks. Based on these beneficial bacteria, microbial inoculants can be developed for use in sustainable agricultural and horticultural production.