A measurement method with calotte cube was proposed to realize the high-precision calibration of size error in industrial computer tomography (CT) system. Using the traceability of calotte cube, the measurement of the repeatability error, probing error and length measurement error of industrial CT system was carried out to increase the acceptance of CT as a metrological method. The main error factors, including the material absorption, projection number and integration time and so on, had been studied in detail. Experimental results show that the proposed measurement method provides a feasible way to measure the size error of industrial CT system. Compared with the measurement results with invar 27- sphere gauge, a high accuracy in the order of microns is realized with the proposed method based on calotte cube. Differing from the invar 27-sphere gauge method, the material particularity of calotte cube (material of metallic titanium) could introduce beam hardening effect, the study on the influence of material absorption and structural specificity on the measurement, which provides significant reference for the measurement of metallic samples, is necessary.