Rac-GTPase-activating protein 1 (RACGAP1) is a member of the Rho GTPase-activating protein (GAP) family, which is involved in the process of cytokinesis. But its precise function in clear cell renal cell carcinoma (ccRCC) has not been extensively investigated. In this study, we found that RACGAP1 was regulated by centrosomal protein CEP55 and markedly facilitated the growth and progression of ccRCC in vitro and in vivo. In addition, RACGAP1 knockdown induces G1 phase arrest, resulting in mitotic disorder and subsequent apoptosis. These findings indicated that RACGAP1, a cell cycle-related gene, is crucial for the survival and growth of ccRCC. Furthermore, renal cancer is closely associated with metabolic processes. As demonstrated by our serum-targeted metabolomics study, RACGAP1 dysfunction altered the levels of multiple amino acids/amino acid derivatives, acylcarnitines, fatty acids/acyls, nucleotides and their metabolites. Spatial metabolomics data further confirmed that down-regulation of RACGAP1 expression could inhibit ccRCC growth not only by reprogramming fatty acid and nucleotide metabolism, but also by interfering with lipid metabolism. More importantly, we detected higher levels of glutamine, acylcarnitines and lipids in the tumor margin region, suggesting intra-tumor metabolic heterogeneity in ccRCC. In conclusion, this study elucidated the biological function of RACGAP1 in promoting ccRCC progression, and revealed the regulatory mechanism of RACGAP1 in interfering with metabolic pathways from the perspective of multidimensional metabolomics. These findings will provide new targets and a theoretical basis for the treatment of RCC.