A system for controlling a motor of a hybrid vehicle determines a current of a first axis and a current of a second axis according to a driving condition, converts the currents of the first and second axes into a 3-phase AC current, and drives the motor by applying the 3-phase AC current to the motor, and includes: a revised temperature calculation module that calculates a revised temperature in order to compensate a torque error according to counter electromotive force dispersion of the motor; and a current determination module that determines the currents of the first and second axes by substituting the corrected temperature to a current map for each temperature and by using a demand torque at a present driving condition, a present speed of the motor, and a maximum counter magnetic flux of the motor.