Objective To compare the clinical value of ultrasound-guided fine needle aspiration cytology, elastography and MRI in the diagnosis of thyroid cancer. Methods The clinical data of 120 patients with thyroid nodules admitted to our hospital from January 2016 to February 2018 in our hospital were analyzed retrospectively. All patients were given surgical resection, a total of 135 thyroid nodules, and all patients were examined by ultrasonic elastography, ultrasound-guided fine needle aspiration cytology and MRI. According to the nodules size, they were divided into group A (nodule > 1cm) and group B (nodule ≤ 1cm). The surgical results were taken as the gold standard to compare and study the above test results, and the accuracy and sensitivity, specificity, accuracy, positive (negative) predictive value, and Kappa value (consistency) of thyroid cancer were analyzed. Results The sensitivity, specificity, accuracy, positive predictive value and negative predictive value of ultrasound-guided fine needle aspiration biopsy in the thyroid cancer diagnosis were 0.917, 0.846, 0.904, 0.962 and 0.710. The sensitivity specificity, accuracy, positive predictive value and negative predictive value of ultrasonic elastography for thyroid cancer diagnosis were 0.927, 0.885, 0.919, 0.971 and 0.742. The sensitivity specificity, accuracy, positive predictive value and negative predictive value of MRI for thyroid cancer diagnosis were 0.908, 0.769, 0.881, 0.943 and 0.667. The sensitivity of the three diagnostic methods in group A was higher than that in group B. Conclusion Ultrasound-guided fine needle aspiration cytology, elastography and MRI have certain clinical diagnostic value for thyroid cancer, and the larger the thyroid gland, the better it is detected.