A method and a system for providing calibration for a polychromatic photon counting detector forward counting model. Measurements with multiple materials and known path lengths are used to calibrate the photon counting detector counting response of the forward model. The flux independent weighted bin response function is estimated using the expectation maximization method, and then used to estimate the pileup correction terms at plural tube voltage settings for each detector pixel. The beam hardening corrections are then applied to the measured projection data sinogram, and the corrected sinogram is reconstructed to the counting image at the selected single energy.