The aim of the study was to explore the value of 3-D shear wave elastography (SWE) in differentiating malignant from benign thyroid nodules. A total of 188 patients with 216 nodules who underwent conventional ultrasound, 2-D SWE and 3-D SWE were included in this study. All patients underwent surgical excision, and the pathological results were the gold standard. Receiver operating characteristic (ROC) curves of the American College of Radiology's Thyroid Imaging Reporting and Data System (ACR TI-RADS), 2-D SWE and 3-D SWE were plotted, and the areas under the curves (AUCs) were compared using a Z-test. There were 62 benign thyroid nodules and 154 malignant thyroid nodules in this study. Young's modulus (E, E, E, E) values of thyroid malignant nodules in different sections of 2-D SWE and 3-D SWE were significantly higher than those of thyroid benign nodules (p < 0.001). The AUC of Ein 2-D SWE transverse sections was significantly lower than that in 3-D SWE transverse sections and 3-D SWE sagittal sections (0.768 vs. 0.831 and 0.844, p < 0.05). The AUC of 3-D S-Ecombined with ACR TI-RADS was 0.859; the specificity increased from 54.84% to 85.71%, and the diagnostic accuracy increased from 74.54% to 85.19%, compared with ACR TI-RADS. The difference was statistically significant (p < 0.05). Three-dimensional SWE combined with ACR TI-RADS for the diagnosis of thyroid nodules significantly improved the diagnostic ability of ACR TI-RADS, and was significantly better than 2-D SWE combined with ACR TI-RADS.