Objective Accurate preoperative characterization of adnexal masses is essential for optimal patient management. Two-dimensional ultrasonography (USG) based "International Ovarian Tumuor Analysis Simple Rules (IOTA-SR)" are used primarily in clinical practice. Three-dimensional (3D) USG is an emerging modality. The authors conducted this study to compare the performance of 3D USG with IOTA-SR for preoperative differentiation of benign and malignant adnexal masses. Methods This prospective observational study recruited 84 patients with adnexal masses undergoing surgical management. IOTA-SR and 3D USG with power Doppler examination were applied to characterize the masses and correlated with histopathology. Logistic regression analysis defined individual 2D and 3D USG parameters' significance in predicting malignancy. The receiver operating characteristic (ROC) curve was plotted for significant variables, and area under the curves (AUCs) with cut-off values were calculated using the Youden index. Results Out of the 84 adnexal masses, 41 were benign and 43 were malignant. IOTA-SR were conclusive in 88.1% (74/84) cases, with a sensitivity of 83.78% (95% confidence interval [CI]: 67.99-93.81%) and specificity of 89.19% (95% CI: 74.58-96.97%). The sensitivity and specificity of 3D USG with power Doppler were 84% and 88%, respectively, with an AUC of 0.96 (95% CI: 0.92-0.99). Ten cases were inconclusive by the IOTA-SR, and 3D USG could further correctly differentiate four of these cases. Conclusion The diagnostic performance of both techniques is comparable. With good diagnostic performance and easy applicability, IOTA-SR remain the standard of care. 3D USG, although a more objective assessment, requires further validation and standardization.