In order to improve the measurement accuracy of inverse fringe, the measurement method based on the three frequencies temporal phase compensation algorithm is proposed to alleviate the nonlinear error of projector-camera measurement system. Two sets of structured light fringes with specific phase offset are projected onto the testing object, and three frequencies temporal phase unwrapping method is used to obtain the unwrapped phase. The system nonlinear phase errors measured by the two sets of fringes with specific phase offset have the characteristics of the same absolute value and opposite sign. So the effect of the system nonlinear error can be eliminated or alleviated by the simple arithmetic calculation, and the measurement accuracy can be improved. The analog simulation and real object contrast experiments are designed to verify the proposed method. Phase standard deviations in the experiments are 6.6122×10-4 rad and 0.0087 rad, respectively. The experiments results show that the proposed method has a great improvement in inverse fringe measurement accuracy, and the validity of proposed method is verified.