Although multispectral and hyperspectral imaging acquisitions are applied in numerous fields, the existing spectral imaging systems suffer from either low temporal or spatial resolution. In this study, a new multispectral imaging system-camera array based multispectral super resolution imaging system (CAMSRIS) is proposed that can simultaneously achieve multispectral imaging with high temporal and spatial resolutions. The proposed registration algorithm is used to align pairs of different peripheral and central view images. A novel, super-resolution, spectral-clustering-based image reconstruction algorithm was developed for the proposed CAMSRIS to improve the spatial resolution of the acquired images and preserve the exact spectral information without introducing false information. The reconstructed results showed that the spatial and spectral quality and operational efficiency of the proposed system are better than those of a multispectral filter array (MSFA) based on different multispectral datasets. The PSNR of the multispectral super-resolution images obtained by the proposed method were respectively higher by 2.03 and 1.93 dB than those of GAP-TV and DeSCI, and the execution time was significantly shortened by approximately 54.55 s and 9820.19 s when the CAMSI dataset was used. The feasibility of the proposed system was verified in practical applications based on different scenes captured by the self-built system.