Wax gourd is an important horticultural crop, and auxin plays a crucial role in its growth and development. However, excessive concentrations of auxin can inhibit plant growth. In this study, we investigated the phenotypic characteristics and conducted a transcriptomic analysis of wax gourd embryonic root development under high auxin concentration. Phenotypic observations revealed that as auxin concentration increased, the primary root of the wax gourd radicle became shorter, the number of lateral roots increased, and the length of lateral roots fluctuated. Transcriptomic analysis identified 1,305 differentially expressed genes (DEGs), including 43 genes associated with auxin, as determined by GO and KEGG annotations. We further focused on 10 key genes with significant differential expression and validated the results using qRT-PCR, which aligned with the transcriptomic date. Notably, the expression of ABCB increased with higher IAA concentrations, while PILS7, LAX3, IAA16, FRQ1, and MYBS3 showed significant downregulation at 600 μM IAA. Conversely, SAUR32 and SAUR71 were significantly upregulated under the same conditions, while the expression of PIN3 and KRP1 exhibited variable patterns. These findings suggest that these genes are key regulators of wax gourd embryonic root responses to high auxin concentration. This study provides valuable insights into the molecular mechanism underlying auxin-induced stress in wax gourd and lays a foundation for further research on its response mechanisms.