Metabolomics is frequently used in the analysis of the dynamic changes within small molecules in response to the disturbance in an organism. It has been extensively used in various fields involving human diseases. To better evaluate the antioxidant capacity, cells subjected to oxidative stress were cultured, and the intracellular metabolites were prepared using HSDE (high-speed shear dispersing emulsifier)-assisted extraction. The metabolites were then analyzed under optimized chromatographic conditions. Partial least squares discriminate analysis was used to analyze the data. A new intracellular metabolomic approach was established, and four potential metabolic biomarkers for repairing oxidative stress were found. The antioxidant activities of Cynomorium songaricum was successfully evaluated using the intracellular metabolomic approach, indicating the feasibility of the proposed approach as an effective tool for evaluating the antioxidant capacity.