For a 3D C-arm computed tomography (CT) system, actual path of the scanner may deviate from the idea circle geometry because of mechanicalinstability, leading to perturbation artifacts in reconstructed images. In this paper, we proposed a modified FBP method for the perturbed trajectories taking into account 6 perturbation parameters without tassuming any condition to be ideal. The preliminary studies demonstrated that this algorithm can acquire promising reconstruction image quality even when the perturbations are relatively large. The comparison of performances among different perturbation parameters is useful for constructing a C-arm CT system.