Grafting is a useful cultivation technology to resist abiotic and biotic stresses and is an integral part of citrus production. However, some widely utilized rootstocks may still exhibit graft incompatibility in the orchard. ‘Hongmian miyou’ (Citrus maxima (Burm.) Merrill) is mutated from ‘Guanxi miyou’, but these two scions showed different compatibility with available Poncirus trifoliata rootstock. Foliage etiolation is an observed symptom of graft incompatibility, but its mechanism remains poorly understood. This study is the first to investigate the morphological, physiological, and anatomical differences between compatible and incompatible grafts, and perform transcriptome profiling at crucial stages of the foliage etiolation process. Based on comprehensive analyses, hormonal balance was disordered, and two rate-limiting genes, NCED3 (9-cis-epoxycarotenoid dioxygenase 3) and NCED5, being responsible for ABA (abscisic acid) accumulation, were highlighted. Further correlation analysis indicated that IAA (indole-3-acetic acid) and ABA were the most likely inducers of the expression of stress-related genes. In addition, excessive starch accumulation was observed in the lamina and midribs of leaves of incompatible grafts. These results provide a new insight into the role of hormonal balance and ABA biosynthesis genes in regulating and contributing to graft incompatibility, and will further define and deploy candidate genes to explore the mechanisms underlying citrus rootstock–scion interactions.

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