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Water deficit is one of the main limiting factors for apple growth and production. Root architecture plays an important role in drought tolerance of plants. However, little is known about the molecular basis of root system in apple trees under drought. In this study, we compared root morphology of two widely used rootstocks of apple (R3 and Malus sieversii) under drought. Our results suggested that M. sieversiiis more tolerant to drought than R3, since M. sieversiihad a higher ratio of root to shoot as well as root hydraulic conductivity under long-term drought conditions. We then performed whole-genome transcriptomic analysis to figure out the molecular basis of root responses in M. sieversiiunder drought. It was found that genes involved in transcription regulation, signaling or biosynthesis of hormones, and oxidative stress were differentially expressed under drought. Consistent with the gene expression profile, roots of M. sieversiihad higher activities of peroxidase (POD) and superoxide dismutase (SOD) under drought, as well as higher content of abscisic acid (ABA) and lower content of auxin. Taken together, our results revealed the physiological and transcriptomic analyses of M. sieversiiroots in response to drought.