Sugarcane smut, a widespread and destructive disease induced by Sporisorium scitamineum, has a significant effect on sugarcane cultivation. Sphingolipids, crucial components of membranes, play a role in plant resistance regulation. However, the specific function of sphingolipids in sugarcane smut resistance has not been understood. This study revealed that following the S. scitamineum infection, ceramide (Cer) and hydroxyceramide (hCer) levels specifically increased in the sugarcane variety ROC22, along with significant alterations in plant hormone levels. Analysis of lipid composition in S. scitamineum‐sensitive and ‐resistant sugarcane varieties indicated that the resistant variety YT93‐159 had lower Cer and hCer levels compared to the sensitive variety ROC22. Additionally, YT93‐159 displayed an increased level of jasmonoyl‐isoleucine (JA‐Ile) and upregulated the expression of genes linked to the pathway of jasmonic acid (JA). Through experiments using the sugarcane protoplast system, it was observed that exogenous ceramide could influence the expression of genes associated with the salicylic acid and JA pathways. This research was the initial examination into the lipidomics‐based molecular mechanisms underlying sugarcane's resistance to S. scitamineum, offering a theoretical foundation for enhancing sugarcane resistance through genetic engineering.