To compare the influence of cultivar and variety on the phenolic compounds and antioxidant activity (AA) of cherry wines, total phenolic (TP), total flavonoid (TF), total anthocyanin (TA), total tannin (TT), five individual phenolic acids, and AA were determined. An ultra-performance liquid chromatography tandem mass spectrometry (HPLC-DAD/ESI-MS) method was developed for the determination of gallic acid (GAE), p-hydroxybenzoic acid (PHB), chlorogenic acid (CHL), vanillic acid (VAN), and caffeic acid (CAF). A principal component analysis (PCA) and a cluster analysis (CA) were used to analyze differences related to cultivar and variety. The TP, TF, TA, TT, and AA of samples sourced from the Shandong province of China were higher than those from the Jiangsu province. The PCA and CA results showed that phenolic compounds in cherry wines were closely related to cultivar and variety and that cultivar had more influence on the phenolic compounds of cherry wines than variety.