Traditional bioassay‐guided investigation of bioactive compounds from natural products comprises critical steps, such as extraction, repeated column separation, and activity assay. Thus, the development of facile, rapid, and efficient technology is critically important. Here, a HepG2 cell‐based extraction method was first developed to rapidly screen potential antitumor compounds from the seeds ofCassia obtusifolia. Then, an online extraction and enrichment–high‐speed counter‐current chromatography (HSCCC) strategy was fabricated to facilely and efficiently isolate target antitumor compounds, which included direct extraction from solid C. obtusifolia, removal of polar interferences, enrichment of target compounds, and preparative isolation by HSCCC using flow rate stepwise increasing mode. After further purification by Sephadex LH‐20 column, five antitumor anthraquinones, aurantio‐obtusin, 1‐desmethylaurantio‐obtusin, chryso‐obtusin, obtusin, and questin, were obtained for structural characterization and bioassay verification. The results may not only provide new perspectives for facile and rapid investigation of bioactive compounds from complex natural products, but also offer a scientific basis for the potential applications of C. obtusifolia.