To evaluate the diagnostic performance of computed tomography (CT) radiomics analysis for differentiating pleomorphic adenoma (PA), Warthin tumor (WT), and basal cell adenoma (BCA). A total of 189 patients with PA (n = 112), WT (n = 53) and BCA (n = 24) were divided into a training set (n = 133) and a test set (n = 56). The radiomics features were extracted from plain CT and contrast-enhanced CT images. After dimensionality reduction, plain CT, multiphase-enhanced CT, integrated radiomics signature models and radiomics score (Rad-score) were established and calculated. The receiver operating characteristic (ROC) curve analysis was taken for the assessment of the model performance, and then comparison was conducted among these models. Decision curve analysis (DCA) was adopted to assess the clinical benefits of the models. Diagnostic performances including sensitivity, specificity, and accuracy of the radiologists were evaluated. Seven, nine, fourteen, and fourteen optimal features were used to constructed plain scan, arterial phase, venous phase, and integrated radiomics signature models, respectively. ROC analysis showed these four models were able to differentiate PA from BCA and WT, with the area under the ROC curve (AUC) values of 0.79, 0.90, 0.87, and 0.94 in the training set, and 0.79, 0.89, 0.86, and 0.94 in the test set, respectively. The integrated model had better diagnostic performance than single-phase radiomics model, but it had similar diagnostic performance to that of the radiomics model based on the arterial phase (p > 0.05). The sensitivity, specificity, and accuracy in the diagnosis of PA were 0.86, 0.46, and 0.70 for the non-subspecialized radiologist and 0.88, 0.77, and 0.84 for the subspecialized radiologist, respectively. Six venous phase parameters were finally selected in differentiating WT from BCA. The predictive effect of the model was favorable, with AUC value of 0.95, sensitivity of 0.96, specificity of 0.83, and accuracy of 0.92. The sensitivity, specificity, and accuracy in the diagnosis between WT and BCA were 0.26, 0.87, and 0.45 for the non-subspecialized radiologist and 0.85, 0.58, and 0.77 for the subspecialized radiologist, respectively. The CT-based radiomics analysis showed favorable predictive performance for differentiating PA, WT, and BCA, thus may be helpful in the clinical decision-making.