As a traditional Tibetan medicine, Dracocephalum heterophyllum has many benefits, but due to the complicated procedures of separation and purification of its chemical constituents, there are few reports on gingerols. In this study, four antioxidative gingerols were isolated from Dracocephalum heterophyllum by an integrated chromatographic approach. Antioxidant activity was then determined by in vitro experiments and its potential targets of action were investigated. First, the extract was pretreated using silica gel, MCI GEL®CHP20P, and diol and spherical medium pressure columns, while the antioxidant peaks were identified using an online HPLC-1,1-diphenyl-2-picrylhydrazyl system. Then, the antioxidant peaks were directionally separated and purified by high pressure liquid chromatography to obtain four gingerols with a purity higher than 95%, namely 5-methoxy-6-gingerol, 6-shogaol, 6-paradol, and diacetoxy-6-gingerdiol. Finally, 1,1-diphenyl-2-picrylhydrazyl assays and cellular antioxidant experiments were carried out, and molecular docking was used to explore potential antioxidant targets. The isolated gingerols upregulated the activity of antioxidant enzymes, including superoxide dismutase (SOD), heme oxygenase-1 (HO-1) and NADPH oxidase 2 (NOX2), while they had little effect on the activity of nadph:quinone oxidoreductase-1 (NQO1). This method can efficiently prepare and isolate antioxidative gingerols from Dracocephalum heterophyllum, and it can be extended to isolate antioxidants from other natural products.