Passion fruit ( Sims) can be divided into yellow and purple varieties. However, information about coloration and fruit quality between the two varieties is limited. To reveal the underlying mechanism of color formation in this fruit, a combined analysis of the metabolome and transcriptome was conducted in this study. The results showed that most of the evaluated flavonols, anthocyanins, and flavanols were significantly upregulated in purple fruit compared to their levels in yellow fruit. Flavonoid and flavonoid carbonoside accumulation was markedly higher in yellow fruit than in purple fruit. The accumulation of organic acids, phenolic acids, lipids, sugars, and lignans was significantly different in the yellow and purple varieties. These results were consistent with the results from the RNA-Seq profile. This study will enable us to identify genes for targeted genetic engineering to improve the nutritional and market value of passion fruit. In addition, the peel and pulp of passion fruit contained certain health-promoting compounds, highlighting the potential application of passion fruit as a functional food and providing direction for future breeding programs and production.