Objective To explore the value of ultrasound elastography in differential diagnosis of small nodules in patients with chronic lymphocytic thyroiditis (CLT). Methods A retrospective analysis was made for 84 cases of CLT in Beijing Jishuitan Hospital. There were totally 112 thyroid nodules, pathology confirmed 41 cases of benign nodules and 71 cases of malignant nodules. All patients were examined by routine ultrasonography and ultrasound elastography before operation. The value of the two kinds of examination methods for diagnosis of CLT combined with small nodules was analyzed. Results The sensitivity of conventional ultrasonic diagnosis was 74.65%, the specificity was 63.41%, and the accuracy rate was 70.54%. The diagnostic sensitivity of ultrasound elastography was 87.32%, the specificity was 85.37% and the accuracy rate was 86.61%. The sensitivity of conventional ultrasonography combined with ultrasound elastography was 94.37%, the specificity was 97.56% and the accuracy rate was 95.54%. The sensitivity of ultrasonic elastic strain rate ratio was 83.10%, the specificity was 90.24% and the accuracy rate was 85.71%. The ROC curve was used to analyze the diagnostic value of the ultrasonic elastic score and the ultrasonic elastic strain rate ratio for benign and malignant nodules. The results showed that the area under the curve of the ultrasonic elastic score was 0.872, and the area under the elastic strain rate ratio was 0.922. Conclusions Ultrasound elastography can reflect the hardness of thyroid nodules. Both ultrasonic elastic score and ultrasonic elastic strain rate ratio are of high diagnostic value. In practical work, ultrasound elastography and conventional ultrasonography can be combined to improve the diagnostic accuracy of thyroid nodules in the patients with chronic lymphocytic thyroiditis.