Objective To explore the application value of ultrasound and CT in Hashimoto thyroiditis. Methods The ultrasound and CT data of 69 patients (108 nodules) with Hashimoto thyroiditis confirmed by pathology during September 2012 to September 2014 were retrospectively analyzed. The diagnostic accuracy, sensitivity and specificity were compared between the two kinds of diagnostic mehods. The ultrasound and CT signs were analyzed. Results With the pathological diagnosis as the golden standard, the diagnostic accordance rate of ultrasound was 85.19% and of CT was 93.52%. The difference was statistically significant (P<0.05). The ultrasonic signs manifested as asymmetric goiters. The shape of 51 nodules was regular, oval or vertical distribution; Net-shaped, patch-like and nodular changes occurred in 51 cases of thyroid essence shadow. Internal echo changed, including 47 cases manifesting as low echo, 11 cases as high echo, 8 cases as isoecho and 3 cases as mixed echo; There was punctiform, annular or nest-like calcified shadow in 35 cases and acoustic halo in 10 cases. CDFI showed that 64 cases can be detected with blood flow signal. CT findings showed that 59 cases showed simple diffuse changes and density uniformly decreasing which was similar to the density of surrounding soft tissues; 6 cases were with enlargement of the thyroid gland and multiple small nodules; 4 cases were with asymmetric goiters and solitary small nodules. The density reduced, with low density shadow; CT scan showed clear edge of the thyroid and density uniformly decreasing. When enhancement scan was performed, the density of nodule area reduced, with clear boundary with the surrounding tissues, without calcified shadow. Conclusion The accuracy of CT in diagnosis of HT was slightly higher than that of ultrasound, but the specificity of both of them was relatively low. Combined inspection can be used to improve the diagnostic accuracy.