Image intensifiers are used internationally as advanced military night-vision devices. They have better imaging performance in low-light-level conditions than CMOS/CCD. The intensified CMOS (ICMOS) was developed to satisfy the digital demand of image intensifiers. In order to make the ICMOS capable of color imaging in low-light-level conditions, a liquid-crystal tunable filter based color imaging ICMOS was developed. Due to the time-division color imaging scheme, motion artifacts may be introduced when a moving target is in the scene. To solve this problem, a deformable kernel prediction neural network (DKPNN) is proposed for joint denoising and motion artifact removal, and a data generation method which generates images with color-channel motion artifacts is also proposed to train the DKPNN. The results show that, compared with other denoising methods, the proposed DKPNN performed better both on generated noisy data and on real noisy data. Therefore, the proposed DKPNN is more suitable for color ICMOS denoising and motion artifact removal. A new exploration was made for low-light-level color imaging schemes.