An OBC controller for vehicle, a system including the same, and a method thereof are provided. The OBC controller includes a measurement device that measures a voltage of each phase of a three-phase OBC and a controller that calculates an impedance of each phase using a voltage of each phase. The voltage is measured before charging of the three-phase OBC starts. The controller also calculates a charging amount for each phase, the charging amount corresponding to the impedance of each phase, and adjusts charging based on the calculated charging amount for each phase.