Abstract: Deviation of geometric parameter from its design value of flat panel detector computed tomography (CT) would result in image quality degradation. A structural deviation calibration and parameters obtaining algorithm based on projections was developed to improve the accuracy. The algorithm uses a simple calibration phantom and serial projections to adjust the system structure and analytically estimate the geometric CT parameters. Calculations demonstrate that the algorithm is very accurate with the error less than 0.5%, and experiments show high quality images.