AbstractA pilot-scale system of 20 t/h for the treatment of ship’s ballast water and the setup of dissolved hydroxyl radical was introduced in this paper. With this experimental system, the kill efficiencies of bacteria, mono-algae, protozoan reach 100% within 2.67 s when dissolved OH· concentration is 0.6 mg/L. At the same time, the effect of hydroxyl radicals on the photosynthesis pigments of phytoplankton was done. The results indicate that the contents of chlorophyl-a, chlorophyl-b, chlorophyl-c and carotenoid are decreased to 35 ~ 64% within 8.0 s further to the lowest limit of test after 5 min. When dissolved OH· ratio concentration is 0.68 mg/L, the attenuation efficiencies of photosynthesis pigment are 100%. Therefore the invasive marine species can be killed in the process of the inputting and discharge ship’s ballast water.