Aims The purpose of this study was to select phosphorus-efficient apple rootstocks under phosphorus deficiency and to reveal the effects of different apple rootstocks on the rhizosphere bacterial community. Methods and Results We used 83 hybrid lines of Malus robusta Rehd. x Malling 9 (M.9) to investigate their physiological traits and the phosphorus deficiency phenotypes of leaves in response to phosphorus deficiency (0 center dot 1 mmol l(-1) PO43-). All the plants were cultivated in pots in the greenhouse and watered using drip irrigation. In accordance with the results of investigation, we selected the phosphorus-efficient hybrid lines (PE) and the phosphorus-inefficient hybrid lines (PI) to research their root morphology and root hairs (RH). In addition, we used Illumina MiSeq sequencing to determine the bacterial community of the rhizosphere from different rootstocks. The results showed that the PE plants had better growth characteristics and stronger root plasticity than that of the PI plants, and phosphorus deficiency can stimulate the RH growth of PE plants. There was no significant difference in the rhizosphere bacterial diversity, but we found that the bacterial community structure was significantly different at the genus levels; in addition, 89 genera were found to have significant differences between PE and PI plants, especially Bacillus. The PE rhizosphere had more abundant Bacillus compared to the PI. High positive Pearson correlations with the phosphorus concentration in the plantlets of apple rootstocks were detected for the bacterial genera Bacillus (r: 0 center dot 776). Conclusions The phosphorus-efficient apple rootstocks adapted to phosphorus deficiency by shaping the root morphology. Notably, different apple rootstocks showed alteration of the microbes in rhizosphere. Significance and Impact of the Study This study can provide the materials for exploring the mechanism of apple rootstock phosphorus absorption. In accordance with the different bacterial community compositions, we can develop the inoculants to promote nutrient uptake.