In this paper, a method is presented for compensating of manufacturing defects in a Wollaston prism array (WPA) via post data processing. The manufactured WPA usually suffers from unequal internal wedge angles from sub-prism to sub-prism and the formation of tilted interference fringes within each sub-prism. After compensation, the spectral error induced by defects in the Wollaston prism array is significantly reduced so that the performance of a non-scanning Fourier transform spectrometer can be substantially enhanced. Experimental results are presented to demonstrate the method of compensation.