Purpose The aim of this study is to develop and compare performance of radiomics signatures using texture features extracted from noncontrast enhanced CT (NECT) and contrast enhanced CT (CECT) images for preoperative predicting risk categorization and clinical stage of thymomas. Materials and Methods Between January 2010 and October 2018, 199 patients with surgical resection and histopathologically confirmed thymoma were enrolled in this retrospective study. We extracted 841 radiomics features separately from volume of interest (VOI) in NECT and CECT images. The features with poor reproducibility and highly redundancy were removed. Then a least absolute shrinkage and selection operator method (LASSO) logistic regression model with 10-fold cross validation was used for further feature selection and radiomics signatures build. The predictive performances of radiomics signatures were assessed by receiver operating characteristic (ROC) analysis. The areas under the receiver operating characteristic curve (AUC) between radiomics signatures were compared by using Delong test. Result In differentiating high risk thymomas from low risk thymomas, the AUC, sensitivity, and specificity were 0.801(95% CI 0.740–0.863), 0.752 and 0.767 for radiomics signature based on NECT images, and 0.827 (95% CI 0.771 -0.884), 0.798, and 0.722 for radiomics signature based on CECT images. But there was no significant difference (p=0.365) between them. In differentiating advanced stage thymomas from early stage thymomas, the AUC, sensitivity, and specificity were 0.829 (95%CI 0.757-0.900), 0.712, and 0.806 for radiomics signature based on NECT images and 0.860 (95%CI 0.803-0.917), 0.699, and 0.889 for radiomics signature based on CECT images. There was no significant difference (p=0.069) between them. The accuracy was 0.819 for radiomics signature based on NECT images, 0.869 for radiomics signature based on CECT images, and 0.779 for radiologists. Both radiomics signatures had a better performance than radiologists. But there was significant difference (p = 0.025) only between CECT radiomics signature and radiologists. Conclusion Radiomics signatures based on texture analysis from NECT and CECT images could be utilized as noninvasive biomarkers for differentiating high risk thymomas from low risk thymomas and advanced stage thymomas from early stage thymoma. As a quantitative method, radiomics signature can provide complementary diagnostic information and help to plan personalized treatment for patients with thymomas.