To compare thymic features using unenhanced computed tomography (CT) images between children with non-thymomatous ocular myasthenia gravis (OMG) and healthy children and determine the image feature cut-off values to allow differentiation of the two populations. We conducted a retrospective study involving 66 children who underwent chest CT, with 33 having non-thymomatous OMG and 33 healthy children without any abnormality. We recorded CT features of the thymus in each child, including the mean CT attenuation value, thymus area, area ratio, anteroposterior (AP) length, width (W), thickness (T), and transverse diameter (TD). These characteristics were analyzed to distinguish OMG from healthy controls. The receiver operating characteristic (ROC) analysis was used to clarify the best assessment, and the optimal cut-off values were determined. The mean CT attenuation value, the thymus area, area ratio, and TD were significantly different (P < 0.05) between the two groups. The mean CT attenuation value was the most significant characteristic in differentiating OMG and healthy controls (area under the curve [AUC] = 0.70). Using 50.41 as the cut-off value for mean CT attenuation, a specificity of 0.70 and sensitivity of 0.82 was observed for distinguishing the two groups (P = 0.003). Optimal differentiation was achieved by combining more than one characteristic including CT attenuation, thymus area, and TD with an optional area ratio (AUC = 0.72). Non-enhanced CT of the thymus complemented the clinical workup of children with non-thymomatous OMG. The cut-off values of the CT features may allow robust differentiation of OMG children.