A method and a system for compensating an offset of a resolver, may include sampling an output signal of the resolver at a predetermined sampling frequency, comparing magnitudes of the sampled output signals of the resolver, when a difference in magnitude between the sampled output signals of the resolver is greater than a predetermined reference value, controlling the motor by a random pulse width modulation (RPWM) scheme in which switching frequencies of the switching elements in the inverter are arbitrarily changed, and compensating an offset of the resolver coupled to the motor while controlling the motor with the RPWM scheme.