The objective is to develop and validate a combined model for noninvasive preoperative differentiating tumor deposits (TDs) from lymph node metastasis (LNM) in patients with rectal cancer (RC). A total of 204 patients were enrolled and randomly divided into 2 sets (training and validation set) at a ratio of 8:2. Radiomics features of tumor and peritumor fat were extracted by using Pyradiomics software from the axial T2-weighted imaging of MRI. Rad-score based on extracted Radiomics features were calculated by combination of feature selection and the machine learning method. Factors (Rad-score, laboratory test factor, clinical factor, traditional characters of tumor on MRI) with statistical significance were integrated to build a combined model. The combined model was visualized by a nomogram, and its distinguish ability, diagnostic accuracy, and clinical utility were evaluated by the receiver operating characteristic curve (ROC) analysis, calibration curve, and clinical decision curve, respectively. Carbohydrate antigen (CA) 19-9, MRI reported node stage (MRI-N stage), tumor volume (cm3), and Rad-score were all included in the combined model (odds ratio = 3.881 for Rad-score, 2.859 for CA19-9, 0.411 for MRI-N stage, and 1.055 for tumor volume). The distinguish ability of the combined model in the training and validation cohorts was area under the summary receiver operating characteristic curve (AUC) = 0.863, 95% confidence interval (CI): 0.8–0.911 and 0.815, 95% CI: 0.663–0.919, respectively. And the combined model outperformed the clinical model in both training and validation cohorts (AUC = 0.863 vs 0.749, 0.815 vs 0.627, P = .0022, .0302), outperformed the Rad-score model only in training cohorts (AUC = 0.863 vs 0.819, P = .0283). The combined model had highest net benefit and showed good diagnostic accuracy. The combined model incorporating Rad-score and clinical factors could provide a preoperative differentiation of TD from LNM and guide clinicians in making individualized treatment strategy for patients with RC.