Objective To compare differences of characteristics of ultrasonic elasticity imaging for benign and malignant small thyroid nodules with or without Hashimoto thyroiditis (HT). Methods The thyroid nodules with ≤1 cm size and the category 4A, 4B, 4C, and 5 of Thyroid Imaging Reporting and Data System (TI-RADS) were included into this study, and a further examination of real-time elastography was performed. The final diagnosis was relied on the pathological diagnosis. The elasticity score and strain ratio (SR) were recorded and compared between these two groups, respectively. Results Of the 424 nodules, 103 nodules were accompanied with HT (thyroid nodule with HT group), 321 nodules were not accompanied with HT (thyroid nodule without HT group). In the thyroid nodule with HT group, the area under the receiver operator characteristic (ROC) curve (AUCs) of the elasticity score and the SR was 0.685 and 0.676, respectively; the optimal cut offs of the elasticity score and the SR was 3 points and 2.45 respectively, their corresponding sensitivity, specificity, and accuracy was 75.7%, 57.6%, 68.0% and 75.7%, 60.6%, 67.6%, respectively. In the thyroid nodule without HT group, the AUCs of the elasticity score and the SR was 0.692 and 0.692, respectively; the optimal cut offs of the elasticity score and the SR was 4 points and 2.84, respectively; their corresponding sensitivity, specificity, and accuracy was 57.5%, 74.2%, 69.2% and 76.1%, 59.7%, 67.7%, respectively. Conclusions Elastography is helpful in differential diagnosis of benign and malignant small thyroid nodules. While, standards of elasticity score and SR value in differential diagnosis are different between benign and malignant small thyroid nodules with HT and without HT, elasticity score and SR ratio decrease in benign and malignant small thyroid nodules with HT.