Apple production is threatened by cadmium contamination in orchards. Cd accumulation and tolerance in graftedMalusplants is affected by rootstock, scion, and their interaction. This dataset is part of an experiment investigating the molecular mechanism of Cd bioaccumulation and tolerance in different apple rootstock-scion combinations. We exposed four rootstock–scion combinations to Cd treatment consisting of Hanfu and Fuji apple (Malus domestica) scions grafted onto apple rootstocks ofM. baccataorM. micromalus“qingzhoulinqin”. RNA sequencing was conducted in roots and leaves of grafting combinations under 0 or 50 μM CdCl2conditions. A comprehensive transcriptional dataset of affected rootstock, scion, and their interaction among different graft combinations was obtained. This dataset provides new insights in the transcriptional control of Cd bioaccumulation and tolerance in grafting plants regulated by rootstock and scion. Herein, we discuss the molecular mechanism underlying Cd absorption and bioaccumulation.