Pinellia ternata(Thunb.) Breit. (P. ternata) is a very important plant that is commonly used in traditional Chinese medicine. Its corms can be used as medicine and function to alleviate cough, headache, and phlegm. The epidermis ofP. ternatacorms is often light yellow to yellow in color; however, within the range ofP. ternatafound in JingZhou City in Hubei Province, China, there is a form ofP. ternatain which the epidermis of the corm is red. We found that the total flavonoid content of redP. ternatacorms is significantly higher than that of yellowP. ternatacorms. The objective of this study was to understand the molecular mechanisms behind the difference in epidermal color between the two forms ofP. ternata. The results showed that a high content of anthocyanidin was responsible for the red epidermal color inP. ternata, and 15 metabolites, including cyanidin-3-O-rutinoside-5-O-glucoside, cyanidin-3-O-glucoside, and cyanidin-3-O-rutinoside, were screened as potential color markers inP. ternatathrough metabolomic analysis. Based on an analysis of the transcriptome, seven genes, includingPtCHS1,PtCHS2,PtCHI1,PtDFR5,PtANS,PtUPD-GT2, andPtUPD-GT3, were found to have important effects on the biosynthesis of anthocyanins in theP. ternatacorm epidermis. Furthermore, two transcription factors (TFs),bHLH1andbHLH2, may have regulatory functions in the biosynthesis of anthocyanins in redP. ternatacorms. Using an integrative analysis of the metabolomic and transcriptomic data, we identified five genes,PtCHI,PtDFR2,PtUPD-GT1,PtUPD-GT2, andPtUPD-GT3, that may play important roles in the presence of the red epidermis color inP. ternatacorms.