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<i>Catharanthus roseus</i> exhibits vibrant petals and displays robust resistance to disease and drought, making it highly valuable for ornamental and gardening applications. While the application of <i>C. roseus</i> as a source of anticancer drugs has gained considerable attention in recent years, there has been limited investigation into the regulatory mechanism underlying anthocyanin accumulation in the petals of <i>C. roseus</i>. This study comprehensively analyzed the metabolome and transcriptome of three distinct <i>C. roseus</i> varieties exhibiting different petal colors. Out of the 39 identified flavonoids, 10 anthocyanins exhibited significant variations in accumulation, directly contributing to the diverse coloration of <i>C</i>. <i>roseus</i> petals. Among them, malvidin 3-<i>O</i>-glucoside and petunidin 3-<i>O</i>-glucoside were identified as primary contributors to the purple petal phenotype, while peonidin 3-<i>O</i>-glucoside and delphinidin 3-<i>O</i>-glucoside exhibited the highest contribution rates to the red petals. Additionally, the variation content of cyanidin 3-<i>O</i>-rutinoside, delphinidin 3-<i>O</i>-glucoside, and petunidin 3-<i>O</i>-rutinoside also influenced the color transformation of <i>C. roseus</i> petals. RNA sequencing identified a total of 4173 differentially expressed genes (DEGs), including 1003 overlapping DEGs. A combined transcriptome and metabolome analysis showed that the coordinately regulated anthocyanin biosynthetic genes including chalcone isomerase (<i>CHS</i>), flavonoid 3′-hydroxylase (<i>F3′H</i>), and dihydroflavonol 4-reductase (<i>DFR</i>) played critical roles in the formation of the anthocyanins. <i>MYB</i> and <i>bHLH</i> transcription factors were also found to be significantly correlated with differences in flower color. These results serve as a foundation for future investigations into anthocyanin biosynthesis and regulatory mechanisms in <i>C. roseus</i>.