The invention provides a method and a device for killing algae and bacteria in the pipeline transportation of marine ballast water. A millipore filter and a tubular high-voltage discharge reaction unit are connected on a transportation pipeline of the marine ballast water in series, the marine ballast water passes through the millipore filter, the diameter of filtration pores is 20 to 50 microns, and larger suspended matters and aquatic organisms entering a pipeline system of the marine ballast water are removed; and the filtered water enters the tubular high-voltage discharge reaction unit, pulse high voltage of 10 to 60 kilovolts is applied between a high-voltage electrode and a ground electrode of the tubular high-voltage discharge reaction unit, high-voltage pulse discharge is generated, the detention time of the ballast water in the tubular high-voltage discharge reaction unit is 0.1 to 2 hours, and the ballast water passing through the tubular high-voltage discharge reaction unit enters a ballast tank. The invention can kill or inactivate foreign pathogens and pests in the ballast water in a pipeline transportation system and lowers or eliminates the marine pollution caused after the ballast water is discharged.