Background Computed tomography (CT) can avoid interference factors and has been imported into some software to measure proptosis clinically as the golden standard. Purpose To establish a new method for semi-automatically measuring the proptosis on CT and evaluate its accuracy and reproducibility. Material and Methods A total of 50 orbital CT images were collected of healthy individuals, 25 patients with Graves ophthalmopathy (GO), and 25 patients with orbital fracture (OF). A new image processing software, MedrawHDC, was developed to semi-automatically measure the proptosis (MedrawHDC method). The classic radiological (CR) method (measuring proptosis with the software called Mimics) and MedrawHDC method were applied in all three groups (measured by observer S). Hertel's exophthalmometer (HE) method was also applied in the GO group. Moreover, two other observers were asked to measure the proptosis using MedrawHDC, to evaluate its reproducibility. Results The MedrawHDC method was highly consistent with the CR method in measuring proptosis (normal group: intraclass correlation coefficient [ICC] = 0.989; GO group: ICC = 0.979; OF group: ICC = 0.979). In the GO group, the value of proptosis measured by two radiological methods were consistent with that measured by the HE method (CR method: ICC = 0.703; MedrawHDC method: ICC = 0.697). Bland–Altman plots showed similar results. The measurements obtained by three observers were highly reproducible (ICC = 0.995). Conclusion The newly established MedrawHDC method, with high accessibility, convenience, and repeatability, is reliable in assessing proptosis. It shows high potential for wide application, having clinical value for scientific evaluation of proptosis.