The hydroxyl radical (${ullet}OH$) scavenging and ferrous ion chelating activities of four isoquinoline alkaloids isolated from Coptis chinensis Franch were studied for the identification of their structural characteristics to scavenge ${ullet}OH$. The ${ullet}OH$ was generated via Fe(II)-catalazed Fenton reaction in this study and the reliable measurement of ${ullet}OH$ scavenging activities of isoquinoline alkaloids were achieved using electron spin resonance (ESR) spectrometry method. At the 1 mM concentration, berberrubine (85%) showed the strongest ${ullet}OH$ scavenging activity and the next were in the decreasing order of coptisine (79%), berberine (23%), and palmatine (22%). The ferrous ion chelating effects of the alkaloids showed similar pattern with their ${ullet}OH$ scavenging effects. These results suggest that ${ullet}OH$ scavenging effects of the alkaloids were closely related to their ferrous ion chelating activities. In addition, metal chelating functional groups such as hydroxy group at C-9 and methylenedioxy group at C-9 and C-10 were thought to contribute to the ${ullet}OH$ scavenging activities of the isoquinoline alkaloids.