Top-grafting is widely used for cultivar renewal in old citrus orchards, yet some hetero-top-grafted combinations show poor tree vigor and restricted growth. However, the physiological mechanisms underlying this growth limitation remain unclear. Here, we investigated carbon allocation, carbohydrate metabolism, phytohormone accumulation, anatomical structure, and multi-omics responses in citrus plants subjected to non-top-grafted, self-top-grafted, and hetero-top-grafted. Hetero-top-grafted plants showed significantly lower aboveground, root, and whole-plant biomass than both non-top-grafted and self-top-grafted plants, with reductions of 41.0%, 38.3%, and 39.9%, respectively, relative to non-top-grafted plants. Stable 13C tracing revealed that hetero-top-grafted caused strong retention of newly fixed carbon in the top-grafted union bark, accompanied by reduced carbon allocation to the roots, indicating impaired downward carbon allocation. Consistently, hetero-top-grafted plants accumulated starch and soluble sugars in the top-grafted union bark, but showed reduced carbohydrate availability in roots. Anatomical observations further revealed swelling, bark cracking, and disrupted phloem structure at the hetero-top-grafted union. Hormone analysis showed increased auxin and abscisic acid contents but decreased cytokinin and gibberellin contents in the union top-grafted union bark, indicating disturbed hormone status. Integrated metabolomic and transcriptomic analyses further revealed coordinated changes in starch and sucrose metabolism, hormone signaling, and phenylpropanoid/flavonoid biosynthesis. These findings support a model in which hetero-top-grafted impairs downward carbon allocation and induces physiological and molecular reprogramming at the graft union, thereby contributing to growth inhibition in citrus.