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Apples are a major horticultural crop worldwide. Grafting techniques are widely utilized in apple production to keep the varieties pure. Interstocks are frequently used in Northern China to achieve intensive apple dwarfing cultivation. High-throughput sequencing was used to investigate differentially expressed genes in the phloem tissues of two different xenograft systems, M (‘Gala’/‘Mac 9’/<i>Malus baccata</i> (L.) Borkh.) and B (<i>‘Gala’</i>/<i>Malus baccata</i> (L.) Borkh.). The results showed that dwarfing interstocks could significantly reduce the height and diameters of apple trees while have few effects on the growth of annual branches. The interstocks were found to regulate the expression of genes related to hormone metabolism and tree body control (<i>GH3.9</i>, <i>PIN1</i>, <i>CKI1</i>, <i>ARP1</i>, <i>GA2ox1</i> and <i>GA20ox1</i>), these effects may attribute the dwarf characters for apple trees with interstocks. Besides, the interstocks reduce photosynthesis-related genes (<i>MADH-ME4</i> and <i>GAPC</i>), promote carbon (C) metabolism gene expression (<i>AATP1</i>, <i>GDH</i> and <i>PFK3</i>), promote the expression of nitrogen (N)-metabolism-related genes (<i>NRT2.7</i>, <i>NADH</i> and <i>GDH</i>) in rootstocks, and improve the expression of genes related to secondary metabolism in scions (<i>DX5</i>, <i>FPS1</i>, <i>TPS21</i> and <i>SRG1</i>). We also concluded that the interstocks acquired early blooming traits due to promotion of the expression of flowering genes in the scion (<i>MOF1</i>, <i>FTIP7</i>, <i>AGL12</i> and <i>AGL24</i>). This study is a valuable resource regarding the molecular mechanisms of dwarf interstocks’ influence on various biological processes and transplantation systems in both scions and rootstocks.