Atractylodes chinensis (DC.) Koidez. (AC) is a type of Atractylodis Rhizoma that is widely used in China to treat diarrhea and arthritis, as well as a nutritional supplement. The objective of this study was to investigate and identify the phytochemicals in the aqueous extract of AC using an ultra-high-performance liquid chromatography (UHPLC)–Orbitrap–HRMS platform based on a non-targeted metabolomic approach. There were 76 compounds in the AC, the majority of which were phenylpropanoids (16) and terpenoids (15). The hierarchical clustering analysis (HCA) and principal component analysis (PCA) results revealed variations across eight AC samples and classified them into four groups. Using Pareto modeling, the orthogonal partial least squares-discriminant analysis (OPLS-DA) identified 11 distinct AC compounds. Furthermore, the antioxidant activity of eight AC samples was assessed using ABTS, DPPH, and OH· methods. The AC samples with concentrations ranging from 0 to 25 mg/mL had no toxic effects on A549 cells. They have a strong therapeutic potential against oxidation-related diseases, and further research on AC is warranted.