Eupatorium adenophorum is widely distributed throughout the world’s tropical and temperate regions. It has become a harmful weed of crops and natural environments. Its leaves contain bioactive compounds such as chlorogenic acid and may be used as feed additives. In this study, chlorogenic acid was extracted and separated from leaves of E. adenophorum. Three chlorogenic acid products were prepared with different purities of 6.11%, 22.17%, and 96.03%. Phytochemical analysis demonstrated that the main toxins of sesquiterpenes were almost completely removed in sample preparation procedure. The three products were evaluated for safety via in vitro and in vivo toxicological studies. All the products exhibited no cytotoxic effects at a dose of 400 μg/mL in an in vitro cell viability assay. When administered in vivo at a single dose up to 1.5 g/kg bw, all three products caused no signs or symptoms of toxicity in mice. These results encourage further exploration of extracts from E. adenophorum in feed additive application.