In order to limit the size of aliasing area caused by distance between filter-array and the detector and improve efficiency of pixel utilization, the filter-array was designed. Filter-array which is diferent from itself in-orbit state is withstanded greater differential pressure in the ground testing experiment, the surface of filter-array changed, which may adversely affect the quality of multi-spectral imaging camera. Baesd on Finite element method , the deformation of the filter-array was analyzed which is attached to original surface of filter-array in Zemax by means of Zernike polynomials. The changes of the modulation transfer function of multi-spectral imaging camera was studied. The results show that under pressure difference, The modulation transfer function of system is not changed significantly and the impact of filter-array′s deformationon on imaging quality of optical system can be negligible.