The apparatus for scanning at least one hyper-spectral image comprises an optical system, the hyper-spectrometer and the relay module. The hyper-spectrometer is disposed apart from the optical system. The optical system can focus an optical image of a target in a focal plane thereof, where the focal plane contains a plurality of row portions of the optical image. The relay module can selectively relay one of the row portions of the optical image to the hyper-spectrometer. Moreover, a method for scanning at least one hyper-spectral image is disclosed in specification.