The dwarfing mechanism in apple clonal rootstocks is driven by complex interactions between anatomical, hormonal, genetic, and phenolic factors, offering potential for advanced genetic manipulation to optimize tree size and enhance orchard productivity. The widespread adoption of dwarfing rootstocks is pivotal to modern commercial apple (Malus × domestica Borkh) orchards due to their ability to control tree size, shorten the juvenile period, and enhance reproductive growth and overall productivity. The underlying mechanisms of rootstock-induced dwarfism are multifaceted and involve interactions between phenotypic, anatomical, genetic, and phytohormonal factors. This review consolidates current understanding, highlighting the importance of auxin (IAA), cytokinins (CKs), gibberellins (GAs), and abscisic acid (ABA) in mediating growth suppression through impaired transport and hormone signaling. The phenotypic impacts, including reduced root growth, shorter sylleptic shoots, and higher floral bud densities, are discussed alongside genetic loci such as Dw1, Dw2, and Dw3, and the influence of key genes/TFs like MdWRKY9, RGL, and PIN. Anatomically, dwarf rootstocks exhibit a higher bark-to-wood ratio and restricted hydraulic conductivity, which contribute to reduced scion vigour. Furthermore, the accumulation of phenolic compounds in the graft union of dwarfing rootstocks further modulates the growth inhibition. These insights lay the groundwork for advanced molecular breeding strategies, incorporating gene-editing technologies to improve dwarf rootstock development, providing avenues for enhanced orchard management and apple productivity.