Naodesheng prescription is a widely used traditional Chinese medicine (TCM), and mainly applied in clinics to treat cerebral arteriosclerosis, ischemic stroke, sequelae of cerebral hemorrhage etc. The present study was designed to investigate the anti-thrombosis effects of this prescription, and to search its bioactive fraction. We evaluated the anti-thrombotic effects by measuring platelet aggregation in rats, and the clotting time and protection rate in mice. The contents of total saponins and flavonoids in the bioactive fraction were determined by UV–vis spectrophotometry. The results showed that Naodesheng has significant anti-thrombotic and anticoagulation effects. The contents of total saponins and flavonoids in the bioactive fraction were 7.885% and 8.434%, respectively. Such study will contribute to further exploration of Naodesheng in the therapy of thrombosis diseases and to its re-development based on the bioactive fraction and ingredients.