Abstract: Large-scale outbreak of Cryptocaryon irritans during cultivations of Larimichthys is a serious threat to the health mariculture, The outbreak caused significant economic losses in China. In experiments at a L. crocea breeding base in Sanduao Sea, Ningde City, Fujian Province, the hydroxyl radicals (-OH) produced by a strong ionization discharge were injected into the pipeline to inactivate Cryptocaryon irritans (100%) rapidly at concentrations of 0.53 mg/L in 6 s and then the solution was discharged into clean water pool stored as L. crocea farming water. L. crocea cultured in ·OH treated seawater had a complete intestinal structure with long and dense intestinal villi and a 100% survival rate. Vibrio, total coliforms and heat-resistant coliforms were not detected in waters from the clean water pool, and the total bacteria was 0 CFU/mL. The water quality met the requirements of Class II by the National Seawater Quality Standard. Moreover, bromate, chloroform, etc. were not detected, and tribromomethane was only 7.84 μg/L, which was much lower than the limitation of 100 μg/L set by the Sanitary Standards for Drinking Water. Thus, the method can be used safely for marine ecology.