An apparatus and method for precisely controlling production, injection, and removal of disinfectants using electrolysis according to the flow rate of ballast water are provided, where the ballast water flows into or is discharged from the ballast tank to manage the ballast water or ships so that destruction or disruption of marine ecosystems can be prevented. An apparatus for treating ballast water and treatment method using the same are provided, the apparatus including: an electrolysis module for producing concentration-controlled sodium hypochlorite; a gas-liquid separator for separating hydrogen gas; a micro bubble generator for mixing and supplying reducing agents while reducing residual chlorine; a vortex generator for generating vortex; and a control system. The control system controls a salinometer, a flow rate meter, a residual chlorine meter, a seawater supply pump, flow rate control valves, an electrolysis module, a residual chlorine meter, a micro bubble generator, and an injection pump.