Three-dimensional measurement based on fringe projection has been widely used. However, the gamma nonlinearity and system nonlinearities usually result in significant phase error. Furthermore, there are various gamma values due to the non-uniform brightness distribution of the projector and nonlinear factors of the system, which makes the problem more complicated. To solve this problem, a sub-area compensation method based on multiple gamma values is proposed. In the beginning, a uniform image is projected on a standard whiteboard with a smooth surface. The obtained image is partitioned by using histogram statistics. Then, different phase error models are established for different regions. Finally, the phase error is compensated according to the regions. By applying this method, the accuracy of the phase algorithm is greatly improved. The method is simple and convenient compared with the existing methods.