Caesalpinia sappan L. is an oriental medicinal plant distributed in the Asia Pacific region including India, Malaysia, and China. The dried heartwood of Caesalpinia sappan has been traditionally used as an analgesic and anti-inflammatory drug. In this study, the effects of extract methods of C. sappan on contents of total polyphenols and flavonoids, antioxidant activity, and cytotoxic activity were evaluated. As a result, hot water extract from C. sappan (CSWE) significantly exhibited contents of total polyphenols and flavonoids (22.6 mg GAE/g and 14.5 mg QE/g) higher than 70% ethanol extract (CSEE) (17.6 mg GAE/g and 13.2 mg QE/g). However, CSEE showed greater antioxidant activity than CSWE in both DPPH and ABTS. Also, the cytotoxicity of C. sappan against three kinds of cancer cell lines was higher in CSEE than in CSWE. These results show that ethanol extract is a better extract method than hot water method to maintain antioxidant and anti-cancer activities.