The effects of 40 Chinese herbs on Microcystis aeruginosa growth were monitored spectrophotometrically. Golden thread (Coptis chinensis) exhibited the best inhibitory effects. Cell density of M. aeruginosa decreased with the increasing concentrations of golden thread and the prolongation of exposure time. Decreases in protein content, carbohydrate content, and chlorophyll a content were observed in a golden thread concentration-dependent manner after 96 h exposure. Changes in cell density, protein content, carbohydrate content, and chlorophyll a content of M. aeruginosa exposed to berberine, the main component of golden thread, were also investigated. It was observed that berberine exhibited the same inhibitory effects on M. aeruginosa. The results suggested that golden thread could inhibit M. aeruginosas growth effectively, and berberine might be the main allelochemical implementing the inhibitory effects of golden thread.