A simple and efficient compensation method for the full correction of both the anisotropic and isotropic nonuniformity of the light phase retardance in a liquid crystal (LC) layer is presented. This is achieved by accurate measurement of the spatial variation of the LC layer's thickness with the help of a calibrated liquid crystal wedge, rather than solely relying on the light intensity profile recorded using two crossed polarizers. Local phase retardance as a function of the applied voltage is calculated with its LC thickness and a set of reference data measured from the intensity of the reflected light using two crossed polarizers. Compensation of the corresponding phase nonuniformity is realized by applying adjusted local voltage signals for different grey levels. To demonstrate its effectiveness, the proposed method is applied to improve the performance of a phase-only liquid crystal on silicon (LCOS) spatial light modulator (SLM). The power of the first diffraction order measured with the binary phase gratings compensated by this method is compared with that compensated by the conventional crossed-polarizer method. The results show that the phase compensation method proposed here can increase the dynamic range of the first order diffraction power significantly from 15~21 dB to over 38 dB, while the crossed-polarizer method can only increase it to 23 dB.