Abstract: In order to ensure the measurement accuracy of the Micro-Computed Tomography (Micro-CT) system, a combined measurement mode of the calibrator and the sample was adapted to design the combined calibrator which can be used for the combined measurement, and a method to correct the proportional error and the threshold error in the measurement process of the Micro-CT system was proposed. Without changing the scanning parameters of the Micro-CT system, the samples of polytetrafluoroethylene, a light material commonly used in aerospace, were measured independently and compared with the measurements based on the combined calibrator. The results show that compared with the sample independent measurement method, the proposed method can effectively reduce the measurement error of 1 μm~4 μm and has better robustness.