<p>Since the beginning of civilization, fruit and nut trees have been propagated asexually. Among the asexual methods of propagation, grafting causes several physiological, biochemical, and molecular alterations in plants to impart precocity, productivity, and tolerance to biotic and abiotic stress and is superior to other methods of propagation. Despite its beneficial effects, the poor communication between rootstock and scion leads to graft incompatibility, causing the fruit plant to be less productive, and in the long run, it leads to the death of the plant. The cause of scion-rootstock incompatibility is due to poor resistance, inadequate genetic predisposition, physiological or biological variables, lignification in the graft union, inadequate graft formation, insufficient cell identification between union tissues, and metabolic variations between the scion and rootstock. Numerous critical physiological and chemical processes in plants at the graft union site are regulated by plant hormones, including cellular communication, cellular reprogramming, pectin secretion, dedifferentiation, cellular connectivity, and callus formation. Even transcriptome analysis has confirmed the relationship between gene expression related to wound healing and auxin synthesis. Numerous alterations in DNA, RNA, and protein also occur at the molecular level. Predictions related to graft incompatibility through secondary metabolites and an understanding of the physiology of graft compatibility are discussed in detail in this review. Moreover, this review focuses on the effects of rootstock on altering the size and vigour of a plant through anatomical, hormonal, and phenolic compound interactions, yield and yield-related parameters, fruit quality, nutrient uptake, etc. An outline of the fundamental physiological, biochemical, and cellular alterations that transpire in horticultural crops subsequent to the attachment of the scion and stock is given in this review.</p>