Despite being primarily utilized for the commercial propagation of durian seedlings, there still needs to be more understanding regarding the histological and biochemical changes that durian plants undergo during compatibility. Further research is required to elucidate this aspect of durian plant biology. The investigation utilized the cleft-grafted 'Monthong' durian cultivar onto indigenous durian rootstock. Examining histological and transverse sections elucidated the three fundamental biological processes involved in graft union formation: scion-rootstock adhesion and wound response, callus bridge construction, and vascular reconnection essential for effective wound healing. These changes are related to the appearance of successfully grafted durian with new sprouting, smooth graft union, and dark green leaves. Quantification of endogenous hormones through LC-MS analysis during the process of graft union formation revealed distinct levels of auxins (IAA), cytokinins (zeatin), gibberellins (GA3), and abscisic acid (ABA) at various stages of graft development post-grafting. Low levels of IAA were observed during the wound response, callus cell formation, and callus differentiation. It was accompanied by significantly higher concentrations of zeatin, which were present at all stages, with particularly pronounced levels during callus bridge formation and vascular reconnection. Upon completion of the union formation, the highest levels of IAA, zeatin, and GA3 were observed simultaneously with the emergence of a new sprout in the graft, coinciding with the whole connection of the new vascular cambium between the scion and rootstock. After the grafting, ABA appeared only three days later, at the time of the wound response. The phenolic compounds in the durian graft union decreased gradually after the vascular cambium of the scion and rootstock had become fully connected, following the callus formation and proliferation period. Total non-structural carbohydrates (TNC) levels at the graft union area peaked during the initial wound response phase and gradually declined as callus bridge formation and wound healing progressed. TNC increased during vascular cambium formation and decreased when the graft produced new sprouts. The anatomical and visual characteristics, endogenous hormones, phenolic acid, and TNC were influential in the modulation of graft union formation and the early growth of the 'Monthong' durian cleft graft on the indigenous rootstock. These parameters show the potential markers detected since the early nursery stage of durian graft.