An engine clutch control system for a hybrid vehicle has a power source including an engine and a motor, an engine clutch between the engine and the motor, a traveling information detector that detects traveling information including at least one of the vehicle speed, shift gear, displacement of the accelerator pedal, and displacement of the brake pedal, and a hybrid controller that selects an EV mode or HEV mode by controlling disengagement or engagement of the engine clutch. A method of controlling the engine clutch includes determining whether there is a request for changing into the HEV mode from the EV mode; determining a reference speed from traveling inertia of the vehicle and inertia of the engine and the motor; determining a desired speed for controlling the determined reference speed; and calculating transmission torque of the engine clutch.