The advanced imaging technique, which leads to unquestionable improved clarity of sample structure, however, is highly vulnerable to systematic and random errors. These errors are fundamental obstacles to a full realization of the next-generation photon science since they can lead to reduced spatial resolution and even misinterpretation of the underlying sample structures. In this work, we target on the most common experimental error which is the center of rotation shift, we formulate new physical models to capture its experimental setups, then we devise new mathematical optimization formulations for robust inversion of complex sample. The numerical results are demonstrated on both synthetic and real data.