Background: It is of great importance to predict the early recurrence (ER) of hepatocellular carcinoma (HCC) after hepatectomy using preoperative imaging modalities. Nevertheless, no comparative studies have been conducted to determine which modality, CT or MRI with radiomics analysis, is more effective. Methods: We retrospectively enrolled 119 HCC patients who underwent preoperative CT and MRI. A total of 3776 CT features and 4720 MRI features were extracted from the whole tumor. The minimum redundancy and maximum relevance algorithm (MRMR) and least absolute shrinkage and selection operator (LASSO) regression were applied for feature selection, then support vector machines (SVMs) were applied for model construction. Multivariable logistic regression analysis was employed to construct combined models that integrate clinical–radiological–pathological (CRP) traits and radscore. Receiver operating characteristic (ROC) curves, calibration curves, and decision curve analysis (DCA) were used to compare the efficacy of CT, MRI, and CT and MRI models in the test cohort. Results: The CT model and MRI model showed no significant difference in the prediction of ER in HCC patients (p =0.911). RadiomicsCT&MRIdemonstrated a superior predictive performance than either RadiomicsCTor RadiomicsMRIalone (p= 0.032, 0.039). The combined CT and MRI model can significantly stratify patients at high risk of ER (area under the curve (AUC) of 0.951 in the training set and 0.955 in the test set) than the CT model (AUC of 0.894 and 0.784) and the MRI model (AUC of 0.856 and 0.787). DCA demonstrated that the CT and MRI model provided a greater net benefit than the models without radiomics analysis. Conclusions: No significant difference was found in predicting the ER of HCC between CT models and MRI models. However, the multimodal radiomics model derived from CT and MRI can significantly improve the prediction of ER in HCC patients after resection.