The plant Zantedeschia hybrida is colorful and suitable for cut flowers and potted plants. This study employed a colorimetric method for the determination of spathe color phenotypes in 27 Z. hybrida cultivars and classified them into six major color classes. To characterize the coloration mechanism of the Z. hybrida spathe, this study explored the main colorants and pigment distribution using high-performance liquid chromatography (HPLC) with photodiode array detection (DAD) and electrospray ionization mass spectrometry (ESI-MS), ultra-performance liquid chromatography/hybrid triple quadrupole linear ion trap mass spectrometry (UPLC-Q-TRAP-MS), and tissue sections. The results showed that flavonoids were colorants in the spathes of different color groups and that cyanidin (Cy) was the main colorant, whereas carotenoids were not detected in the spathe. Total anthocyanin (TA) content was negatively correlated with lightness (L*) of coloration, such that a spathe with a higher TA and thicker pigmented cell layer showed a deeper color; however, there was no correlation between deep coloration in a spathe and flattened upper epidermal cells. The difference in TA was the main reason for the color variation among Z. hybrida of different color groups, whereas the total flavones and flavonols (TF) played a key role in the coloration of the orange and yellow group.