To assess the value of conventional ultrasound, conventional strain elastography (CSE) and acoustic radiation force impulse (ARFI) elastography in differentiating likelihood of malignancy for Bethesda category III thyroid nodules. 103 thyroid nodules with Bethesda category III results on fine-needle aspiration cytology (FNAC) in 103 patients were included and all were pathologically confirmed after surgery. Conventional ultrasound, CSE and ARFI elastography including ARFI imaging and point shear wave speed (SWS) measurement were performed. Univariate and multivariate analyses were performed to identify the independent factors associated with malignancy. Area under the receiver operating characteristic curve (Az) was calculated to assess the diagnostic performance. Pathologically, 65 nodules were benign and 38 were malignant. Significant differences were found between benign and malignant nodules in ARFI. The cut-off points were ARFI imaging grade ≥ 4, SWS > 2.94 m/s and SWS ratio > 1.09, respectively. ARFI imaging (Az: 0.861) had the highest diagnostic performance to differentiate malignant from benign nodules, following by conventional ultrasound (Az: 0.606 - 0.744), CSE (Az: 0.660) and point SWS measurement (Az: 0.725 - 0.735). Multivariate logistic regression analysis showed that ARFI imaging grade ≥ 4 was the most significant independent predictor. The combination of ARFI imaging with point SWS measurement significantly improved the specificity (100% vs. 80.0%) and positive predictive value (100 % vs. 72.9%) in comparison with ARFI imaging alone. ARFI elastography is a useful tool in differentiating malignant from benign thyroid nodules with Bethesda category III results on FNAC.