A method of controlling an on-board charger (OBC) and an OBC system are capable of improving efficiency of the OBC by controlling a DC link voltage such that a DC-DC LLC converter of an ecofriendly vehicle always operates at a resonance frequency. The method includes: detecting a switching turn-on time of a switching unit and a conduction time of a diode, comparing the switching turn-on time with the conduction time, comparing a point of time when the switching unit is turned on with a point of time when the diode becomes conductive, determining an operating frequency region of the switching unit, and controlling a voltage of an input terminal of the LLC converter such that a switching frequency of the switching unit is in a resonance frequency region of the LLC converter according to the determined operating frequency region.