Latest generation of dual-channel spaceborne hyperspectral imager based on visible near infrared (VNIR) and short wave infrared (SWIR) uses the field slitter to separate VNIR and SWIR channels into several sub-fields, and each sub-field image has different ground area at the same time. When using motion compensation technology to improve signal to noise ratio of the instrument, the observation angles of each sub-field are different, which leads to more complicated mismatch of images and make it impossible to get the continuous VNIR-SWIR spectrum of the ground pixel. The rule of image distortion and dual-channel mismatch quantitatively was analyzed by Rigorous imaging model, and the registration scheme by using geometric orientation of each sub-field separately as well as the phase correlation method was proposed on this basis. Verification based on dual-channel spaceborne hyperspectral simulated data of Dongtianshan under motion compensation was performed. The result shows that registration accuracy of traditional scheme based on correlation of images reaches 3.9 pixel, which means the continuous VNIR-SWIR spectrum of the ground pixel is still unavailable. The registration accuracy of the scheme proposed by this paper reaches 0.3 pixel, and the reflectance spectrum overlap ratio error of the overlapping bands of VNIR and SWIR reduces from 41.5% to 1.2%.