To improve the detecting precision of the spectral-polarimetric modulator, a high accuracy alignment of the modulator is established.First, based on the modulation principle of the spectral-polarimetric modulator, a method of alignment using three pieces of thick birefringent retarder and an analyzer to correct the errors is proposed in this paper.Then, the corresponding mathematical model is established, and the thickness of the thick birefringent retarder for calibration is designed.Finally, the simulated demonstrations of system alignment and spectral-polarimetric imaging are also presented.The results show that the method is sensitive to the relative rotation angle errors between the polarization devices, which has the ability to realize the precise alignment of the spectral-polarimetric modulator.And the accuracy can reach 0.2°with the input calibration spectrum set in this paper.The method also keeps the advantage of the traditional method, which guarantees the resolution of the reconstructed Stokes parameters.The research provides theoretical reference for the precision alignment of spectral-polarimetric imaging system.