The rapid formation of the graft necrotic layer is crucial for preventing organic substance leakage and warding off external infections, significantly enhancing both the speed and quality of graft healing. This study investigates the impact of LED supplementary lighting on pumpkin-cucumber grafts, unveiling the molecular processes underlying necrotic layer formation. Specifically, three replications were conducted, where post-grafting cucumber seedlings were placed separately in healing chambers with LED light intensities of 0 μmol/(m2·s) and 50 ± 1 μmol/(m2·s) for three days. Anatomical observations, enzyme activity assays, energy product content detection, and a more comprehensive transcriptome sequencing analysis on the graft union of the rootstock and scion were conducted. Anatomical observations revealed that LED supplementary lighting accelerates the formation of the pumpkin-cucumber graft necrotic layer, establishing a complete layer by the second day post-grafting, one day earlier than the control. Additionally, at day 3 post-grafting, the activities of POD and PPO enzymes at the rootstock-scion junction significantly surpassed the control, exhibiting a remarkable increase of 74.12 % and 48.96 %, respectively (p < 0.01). Moreover, soluble sugar and ATP levels were notably higher at day 3 post-grafting in comparison to the control, showing significant differences (p < 0.05). Transcriptomic analysis unveiled that LED supplementary lighting not only enhances scion sugar metabolism but also stimulates the upregulation of sugar synthesis genes (SPP1, RPV1) and starch synthesis genes (AGPS1, WAXY, SBEⅡ), while downregulating the starch degradation gene LECRK71 when compared to the control. This orchestrated modulation leads to the accumulation of sugars and starch, providing substantial energy and material foundation for necrotic layer formation. Furthermore, LED supplementation also influences the hormone signaling transduction pathway in the scion, notably upregulating the gene Os01g0656200 involved in abscisic acid signaling when compared to the control, thereby furthering the formation of the necrotic layer. Overall, our research showed that LED supplementary lighting accelerates the formation of the necrotic layer in pumpkin-cucumber grafts by enhancing enzyme activities, sugar metabolism, genetic pathways related to starch accumulation, and influencing hormone signal transduction pathways, notably upregulating genes involved in abscisic acid signaling, providing a robust molecular foundation for early necrotic layer development compared to control conditions. These research findings not only provide a valuable reference for understanding graft healing mechanisms but also demonstrate the promising prospects of LED modern seedling technology. Additionally, the research, which is limited to specific pumpkin and cucumber varieties in graft experiments, necessitates further exploration to validate its broader applicability across diverse plant varieties and grafting methods.