A system and a method for controlling an engine clutch of a hybrid vehicle are provided which maintain the acceleration of the vehicle substantially constant before and after release of an engine clutch to prevent a driver from feeling a sense of difference due to a change in inertia when the engine clutch is released. When an engine clutch is released to transfer the driving mode of the vehicle from a hybrid electric vehicle (HEV) mode to an electric vehicle (EV) mode, the acceleration of the vehicle before and after release of an engine clutch is maintained substantially constant by adjusting motor torque to be decreased and gently adjusting the motor torque to be suitable for a driver request torque in the EV mode.