Thrombus is a severe health problem all over the world, especially in developing countries. However, there is still no satisfactory antithrombotic therapeutic strategy. Currently, the clinical antithrombotic drugs suffer from several drawbacks such as high rate of bleedings and short half-life, causing allergic reactions or complications, etc. In recent years, small-molecule compounds isolated from natural products with antithrombotic activities become a hot issue in the field of drug research. In this review, we will focus on representative naturally occurring small molecule flavonoids with antithrombotic potency and potential for future therapeutic regimens to combat thrombosis disease.