Food-deceptive flowers primarily use visual signals (such as color) to mimic model plants and deceive insects into achieving pollination.Paphiopedilum micranthumis a food-deceptive orchid that has a pink labellum and two purple petals with a yellow base and has been proven to be pollinated by bumblebees. However, the chemical and molecular bases of the floral color are not well understood. We conducted targeted metabolite profiling and transcriptomic analysis to determine the color signal and its genetic basis inP. micranthum. We found that both anthocyanins and carotenoids contribute significantly to the formation of floral color that determines the color signal. Higher concentrations of anthocyanins (cyanidin and peonidin) and carotenoids (primarily lutein and zeaxanthin) were detected in the petal compared to the labellum. The upregulation of structural genes ofCHS,F3′H,DFRandANSon the anthocyanin biosynthesis pathway in petals was identified, as well as three genes ofLCYE,BCH, andCCD4on the carotenoid biosynthesis pathway. Furthermore, we discovered that threeR2R3-MYBsand onebHLHtranscription factors were co-expressed with the expression of different genes. These genes and transcription factors may be responsible for the spatial color difference ofP. micranthum. Our study emphasizes that the color of this food-deceptive orchids is achieved through specific genes and transcription factors associated with the pigment biosynthesis pathway.