A method of and a system for spectral correction in multi-energy computed tomography are provided to correct reconstructed images, including high-energy CT images and Z (effective atomic number) images, for spectral variations, which include time variations on a scanner due to HVPS drift and scanner to scanner variations due to the beamline component differences. The method uses a copper filter mounted on the detector array for tracking the spectral changes. The method comprises: generating copper ratios; computing working air tables; calculating scales and offsets; and correcting high-energy CT images and Z images using calculated scales and offsets. The method further includes an off-line calibration procedure to generate necessary parameters for the online correction.