The invention provides a ship ballast water treatment method and a discharge reactor. Ballast water firstly reaches a stainless steel filter screen through a water inlet pipeline, and is filtered by a microporous filter to enter the discharge reactor with particle catalyst; pulse high voltage is applied between a high voltage electrode and a ground electrode of the discharge reactor to generate high voltage pulse discharge; oxygen-containing gas is communicated with the discharge reactor during discharging process, the ballast water treated by the discharge reactor enters a ballast cabin via a filter arranged at the outlet of the discharge reactor. The invention enables the plasma generated by discharging to directly and rapidly react with exotic causative agent and harmful aquatic matter in ballast water, and kills and inactivates the exotic causative agent and harmful aquatic matter under a series of online generated physical and chemical efficacies, and accordingly reduces the pollution of the ballast water to the ocean.