Coreopsis tinctoria, also called “snow chrysanthemum” in China, is a flower tea material that has been reported to possess excellent pharmacological properties such as antioxidant and antidiabetic activities. The chemical characteristics of different parts (flowers, buds, seeds, stems, and leaves) of C. tinctoria were investigated based on microwave-assisted extraction and the simultaneous determination of 13 major active compounds by high-performance liquid chromatography, including taxifolin-7-O-glucoside, chlorogenic acid, (R/S)-flavanomarein, isocoreopsin, quercetagetin-7-O-glucoside, isookanin, 5,7,3′,5′-tetrahydroxyflavanone-7-O-glucoside, marein, 3,5-dicaffeoylquinic acid, coreopsin, okanin, 5,7,3′,5′-tetrahydroxyflavanone, and N,N,N,N-tetra-p-coumaroylspermine. Chemometric analysis based on the contents of investigated compounds from 13 samples showed that C. tinctoria and the related flower tea materials, Chrysanthemum morifolium cv “Hangju” and “Gongju,” were in different clusters, and different parts (flowers, buds, seeds, stems, and leaves) of C. tinctoria were obviously different. This study is helpful for the quality control and pharmacological evaluation of different parts from C. tinctoria and its related products.