In this paper, to reduce the non-linear phase error caused by gamma effect of the digital projector, a novel phase difference extraction method is proposed. First, through multi-layer discrete wavelet decomposition (DWT), the components of the original phase difference at different frequencies are extracted. Subsequently, the effective components are taken by the orthogonal matching pursuit (OMP) algorithm, and the phase difference is reconstructed. According to the upper and lower envelopes of the original phase difference extracted by cubic spline interpolation, the residual threshold of OMP is set. According to the results of three-dimensional (3-D) reconstruction experiment on a standard sphere, the proposed method is capable of reducing the errors in the original phase difference and achieving a better imaging result.