Polyphenols are important functional components that have anti-cancer and anti-inflammatory effects. Apple fruit is rich in polyphenols and is one of the dietary sources of polyphenols. The polyphenol components and contents of the peel and pulp of 74 Malus sieversii (Led.) Roem. and 26 Chinese Malus germplasm resources were determined using ultra-high-phase chromatography (UPLC) and liquid chromatography–mass spectrometry (LC–MS). The results showed that 34 components were detected in the peel and 30 in the flesh, and that the polyphenol components and contents of the different germplasm resources were significantly different; the polyphenol content of Malus sieversii (Led.) Roem. was significantly higher than that of the other local varieties, and the polyphenol content in the peel was also higher than that in the flesh. Rutin, quercetin 3-O-arabopyranoside, kaempferol 3-O-rutinoside, and peonidin 3-O-galactoside were detected only in the peel. The total polyphenol content in the peel ranged from 949.76 to 5840.06 mg/kg, and the polyphenol content in the pulp ranged from 367.31 to 5123.10 mg/kg. The cluster analysis of polyphenol components and contents in peel and pulp showed that 100 Malus germplasm resources could be grouped into four categories. Principal component analysis of 34 kinds and 30 kinds of polyphenols in peel and pulp of 100 resources was performed. If the eigenvalue is greater than 1, eight and seven principal components are extracted, respectively. Five Malus resources with high polyphenol content in the peel and pulp were selected: ‘XY-77’ (peel: 5840.06 mg/kg, pulp: 5123.10 mg/kg; ‘LF-09’ (peel: 4692.63 mg/kg, pulp: 3729.79 mg/kg); ‘2012-5’ (peel: 4377.61 mg/kg, pulp: 3847.54 mg/kg); ‘29028’ (peel: 5088.05 mg/kg, pulp: 3994.61 mg/kg); and ‘11-01’ (peel: 5154.45 mg/kg, pulp: 3616.15 mg/kg). These results provide us with information regarding the polyphenol composition and content of the wild apple resources and local cultivars. The high polyphenol content resources obtained by screening can be used as raw materials for the extraction of polyphenol components and functional fruit juice processing and can also be used as parents for functional fruit creation and variety breeding.