Rambutan is a tropical tree and its fruit has several favorable characteristics. To understand how the color of the rambutan fruit peel develops, the transcriptome, flavonoid metabolome, and carotenoid metabolome data of two rambutan cultivars, ‘BY2’ and ‘BY7’, which show yellow and red peels at maturity, respectively, were comprehensively analyzed at three developmental stages. We identified 26 carotenoid components and 53 flavonoid components in these cultivars. Anthocyanins were the main component contributing to the red color of ‘BY7’ after reaching ripeness. The carotenoid content decreased sharply as the fruit matured. Hence, we speculated that flavonols were the main contributors to the yellow color of the ‘BY2’ peel. In total, 6805 differentially expressed genes were screened by transcriptome analysis; the majority of them were enriched in metabolic pathways and the biosynthesis of secondary metabolites. Weighted gene co-expression network analysis results revealed that in addition to MYB and bHLH, ERF, WRKY, MYB-related, and C3H were the main potential transcription factors regulating the color of the rambutan peel. In addition, we also identified 12 structural genes associated with flavonoid biosynthesis. The research findings shed light on the molecular mechanisms of color acquisition in rambutan fruit peels, laying the foundation for the quality control of rambutan and the cultivation of differently colored cultivars of rambutan.