A quantitative Single Photon Computed Emission Tomography (SPECT) reconstruction system for myocardial blood flow quantitation with SPECT or Single Photon Emission Computed Tomography/Computed Tomography (SPECT/CT) dynamic imaging. The present invention solves the problems of physical interference and patient motions in dynamic SPECT imaging to enable the quantitative ability for myocardial blood flow (MBF) and coronary flow reserve (CFR) quantification.