A method and system for controlling charging of a hybrid vehicle are provided. The method includes generating a request to charge a battery by driving a hybrid starter generator (HSG) with power of an engine in an electric vehicle (EV) mode of the hybrid vehicle. In addition, the method includes decreasing torque of the engine to HSG charging engine torque, maintaining the torque of the engine at the HSG charging engine torque, and shifting torque of the HSG into charging-target HSG torque. A pressure of a clutch disposed between the engine and a driving motor of the vehicle is released to interrupt transference of power from the engine to the driving motor. The battery is then charged with power output from the HSG while the HSG is rotating by driving power output from the engine.