State of the art mechanisms being used for achieving diagnostic-quality images under low-dose settings for general CT imaging have the disadvantages that CT images are fixed during the optimization process to generate perfusion maps, which can lead to suboptimal CT images with respect to the perfusion maps generated, although they might appear spatially smooth or denoised. The disclosure herein generally relates to Computer Tomography (CT) scanning, and, more particularly, to a method and system for CT image reconstruction. The system performs modelling an optimization problem for joint estimation of a set of structural CT images and a perfusion map, and further solves the optimization problem for the reconstruction of the CT images of a subject.