An apparatus and method for controlling an engine stop of a hybrid electric vehicle provides an efficient torque in the operation of a hybrid starter generator, by applying a torque of a high efficiency point of the hybrid starter generator according to a drop of engine RPM when the engine is stopped, so as to improve fuel efficiency of a vehicle and damping vibration of the vehicle when the engine is stopped, by generating a negative torque on the hybrid starter generator side in accordance with the drop of the engine RPM when the engine is stopped, and by applying a torque of the point that gives the maximum charging power of the battery through the generated negative torque.