In this study, untargeted metabolomics based on ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) and multivariate statistics were combined to analyze the differences in metabolite composition in the peel and pulp of three apple varieties from Northeast China (Saiwaihong, K9, and Longfeng) using Red Fuji apples as a control. Our aim was to explore the metabolomic profile and characteristic components of the three varieties. The results showed that a total of 239 metabolites were detected in the peel and pulp of the four varieties, including phenols (48.95%), sugars (15.06%), terpenoids (13.81%), vitamin and fatty acids (11.72%), amino acids (7.11%), and nucleotides (3.35%). For each fruit part, the number and types of metabolites and metabolic pathways in the varieties from Northeast China were similar to those of Red Fuji apples, indicating comparable quality characteristics among the four varieties. Differences were observed in the relative contents of metabolites among the four varieties. Principal component analysis and hierarchical clustering analysis indicated that the peel and pulp were grouped into distinct clusters, with clear separation being found among the different varieties for each fruit part, highlighting compositional differences in the metabolites of the peel and pulp. The number of characteristic differential metabolites (CDMs) in the peel and pulp was follows: 19 and 10 for Saiwaihong vs. Red Fuji, 22 and 16 for K9 vs. Red Fuji, and 31 and 20 for Longfeng vs. Red Fuji, respectively, indicating greater differences in metabolite composition between Longfeng and Red fuji for both fruit parts. When comparing the three Northeast apple varieties, the number of differential metabolites in the peel and pulp was as follows: 22 and 22 for Saiwaihong vs. K9, 21 and 21 for Saiwaihong vs. Longfeng, 31 and 15 for K9 vs. Longfeng, respectively. Phenolic compounds were the major class of CDMs in the peel and pulp of apples among the four varieties. Flavanols such as epicatechin and its oligomer exhibited the highest abundance in Saiwaihong, flavonols such as quercetin glycoside showed the highest abundance in K9, and phenolic acids such as chlorogenic acid and neochlorogenic acid presented the highest abundance in Longfeng. The results of this study provide a scientific reference for the precise development of the three apple varieties from Northeast China and for the cultivation and improvement of apple germplasm resources in China.