An online antifouling ship ballast water treatment system includes a ballast water main pipeline, a ballast water branch pipeline, a dispensing pipeline, a filter on the ballast water main pipeline, an electrolysis unit on the ballast water branch pipeline, and a dispensing pump on the dispensing pipeline. Some of seawater introduced into the system is filtered by the filter and flows to the ballast water branch pipeline and the electrolysis unit, some of seawater electrolyzed by the electrolysis unit is reinjected to the filter through the dispensing pump and the dispensing pipeline after a ballast process is completed, and kept in the filter until a next ballast operation, so that growth and propagation of marine organisms in the filter can be inhibited by sodium hypochlorite contained in a TRO solution when a ballast pump stops working. The present invention also provides a ship ballast water treatment method.