Osmotic adjustments play a fundamental role in plant responses to water deficit. For apple (Malus domestica) trees growing in the primary production areas of China, drought and low phosphorus (P) levels are the main sources of abiotic stress. Although tolerance to drought and low P are important breeding goals for cultivar improvement, there is little information on natural variation within Malus for these traits or the molecular mechanisms that may mediate tolerance. In this study, it was found that in plants grown under conditions of osmotic and low P stress, electrolyte leakage and photosynthetic parameters were significantly higher, but chlorophyll concentrations were lower compared with nonstressed plants. These physiological indicators revealed that, under low P condition, the order of osmotic stress resistance (high to low) was Malus sieversii (Ms) → Malus prunifolia (Mp) → Malus hupehensis (Mh). Expression of the phosphorus transporter genes PHT1;7, PHT1;12, and PHT2;1 in the roots and PHT1;12 and PHT4;5 in the leaves was positively correlated with plant osmotic resistance. It is proposed that the highly expressed PHT genes might improve P absorption and transport efficiency, resulting in the high osmotic stress resistance under low P level conditions in Malus species.