Background Clear cell renal cell carcinoma (ccRCC) is a prevalent tumor in the urinary system, presenting a poor prognosis yet being accompanied by a high degree of immune infiltration. Understanding the mechanisms underlying this abnormal infiltration and identifying prognostic biomarkers in this regard is crucial for improving therapeutic outcomes. Methods The expression of GPD1L in ccRCC was analyzed using a common database (TCGA). The expression of GPD1L in ccRCC cell lines and tissue samples was verified by western blotting, real time qPCR and immunohistochemistry. The predictive value of GPD1L was evaluated by survival analysis, ROC curve and Cox regression analysis. We used GO, KEGG and gene set enrichment analysis (GSEA) to verify each other. Then the single cell sequencing dataset (GEO) was further analyzed and verified, and the functional phenotype of GPD1L in ccRCC was explored by functional experiments. In addition, the correlation between the expression level of GPD1L and drug resistance of AKT-mTOR pathway was analyzed based on Genomics of Drug Sensitivity in Cancer database (GDSC). Results We identified glycerol-3-phosphate dehydrogenase 1-like (GPD1L) as a tumor suppressor gene in ccRCC, and downregulation of GPD1L may facilitate the adaptive survival of tumor cells via enhanced regulatory T cells (Tregs) infiltration and lipid metabolism reprogramming in ccRCC. Our results suggest that there is a significantly diminished GPD1L in ccRCC patients with poorer survival probability. Mechanically, a significant negative correlation between GPD1L expression and Tregs infiltration, and GPD1L-related metabolic analysis reflected the correlation between Tregs and lipid metabolism. In addition, GPD1L expression levels also influence the malignant phenotype of ccRCC and the drug resistance to AKT and mTOR targeted therapy. Conclusions Taken together, our results supported GPD1L could be a valuable biomarker for predicting and intervening in ccRCC progression. These insights could shed light on the complex interplay between tumor cell adaptive survival and Treg infiltration, which reflected that the comprehensive and systemic role of GPD1L in ccRCC.