Abstract Background Chronic thromboembolic pulmonary hypertension (CTEPH) is easily misdiagnosed. Three-dimensional (3D) electrical impedance tomography (EIT) can monitor the whole-lung perfusion at the bedside. In this study, three-dimensional electrical impedance tomography (3D-EIT) features in patients with suspected chronic thromboembolic pulmonary hypertension (CTEPH) was investigated, and nomogram models based on clinical and 3D-EIT parameters were constructed to identify CTEPH. Methods Patients with pulmonary hypertension (PH) due to left heart disease and chronic hypoxia were excluded. The enrolled patients were divided into CTEPH and Non-CTEPH groups by confirmatory tests. Then, history and laboratory results were collected and 3D-EIT examination was performed. Out of 70 enrolled patients, 50 cases were used as the training set to construct the nomogram model. Obtained nomogram diagnostic model was calibrated and then evaluated using receiver operating characteristic (ROC) curves, decision curve analysis (DCA), and clinical impact curves (CIC). Results Through a comprehensive univariate analysis, Wald test, Akaike information criterion (AIC), and Bayesian information criterion (BIC), the nomogram model for CTEPH diagnosis based on 50 patients was constructed using venous thromboembolism (VTE) history, D-dimer, maximum of corresponding regional ventilation/perfusion ratio (V/Qmax), range between the maximum and minimum values of regional perfusion (P-Range) and the percentage of ventilation/perfusion match area (VQMatch). The C-index of the nomogram model in the training set was 0.926 (95% CI: 0.859–0.993). In the training set and test set, the nomogram model had a larger area under the curve (AUC) than models containing only VTE history, VTE history + D-dimer and EIT parameters. Both DCA and CIC analyses indicate that this model can provide significant clinical benefits. Conclusions A nomogram model combining clinical and 3D-EIT parameters facilitated the diagnosis of CTEPH. Clinical trial number Not applicable.