In order to develop an improved method of mitigating harmful algal blooms (HABs), we assessed the inhibitory effects of five Chinese traditional herbs, Andrographis paniculata (Burm.f.) Nees, Galla chinensis, Punica granatum L., Cortex phellodendri chinensis and Radix scutellariae, as well as clay modified with herb extract on the growth of two harmful algae, Phaeocystis globosa and Prorocentrum donghaiense. The results showed that the five Chinese herbs had varying effects on the target microalgae and inhibitory rates ranged from -35% to 100% at concentration of 0.3g dry wt./L during 96h treatments. Among the five herbs, G. chinensis exhibited the strongest inhibitory effect, almost 100% on P. globosa and P. donghaiense. The growth of P. globosa and P. donghaiense was completely inhibited by G. chinensis extracts (0.3g dry wt./L) during all growth phases, and lag phase cultures were more sensitive than exponential phase and stationary phase cultures. The highest inhibitory rate (100% inhibition) on P. globosa was observed at lag phase, followed by exponential phase (73.1% inhibition), and stationary phase (57% inhibition). The highest inhibitory rate of 100% on P. donghaiense was also found at lag phase, 40.3% at exponential phase, and 23.4% at stationary phase. Furthermore, modified clay with G. chinensis extract significantly enhanced the inhibitory impact. Modified clay (0.3gL-1) produced 95% of growth inhibition for both algae species at 24h, and maintained the inhibition thereafter. Our study demonstrated that G. chinensis and clays modified with its extract significantly inhibited the growth of harmful species, therefore may provide ideas and another option for control of harmful algal blooms.