Background and Aims Fine-needle aspiration cytology (FNAC) guided by ultrasound is the primary method for preoperative evaluation of thyroid nodules' benign or malignant nature. Its drawback is inadequate sampling, which may lead to misdiagnosis or missed diagnosis. Core needle biopsy (CNB) can compensate for the shortcomings of FNAC, but its disadvantages include increased pain and trauma. Therefore, this study compared the diagnostic efficacy and characteristics of FNAC and CNB to diagnose thyroid nodules, aiming to provide a reference for clinical rational selection.Methods The data of 552 patients who underwent thyroid surgery in Zhongnan Hospital of Wuhan University from November 2020 to November 2022 were retrospectively analyzed. All patients underwent preoperative ultrasound examination and subsequent FNAC and CNB. Thyroidectomy on the affected side was performed within one week after the puncture. Clinical data of patients, ultrasound characteristics of thyroid nodules, preoperative cytology, histopathology, and postoperative routine pathology results were collected. Postoperative routine pathology was used as the gold standard to analyze the diagnostic efficacy of FNAC and CNB.Results Overall, FNAC and CNB showed similar sensitivity, specificity, and accuracy in diagnosing thyroid nodules, with no statistically significant differences (88.7% vs. 91.4%, P=0.283; 90.6% vs. 97.4%, P=0.226; 85.3% vs. 89.1%, P=0.058). CNB was superior to FNAC in distinguishing between benign and malignant follicular tumors (P=0.024). When the nodule diameter was ≤2.0 cm, there was generally no difference in diagnostic efficacy between FNAC and CNB. When the nodule diameter was >2.0 cm, the sensitivity of CNB was significantly higher than that of FNAC (95.0% vs. 79.2%, P<0.01), and the combined diagnosis of both further increased the sensitivity to 99.2%. For the diagnosis of calcified nodules, cystic nodules, and nodules with rich vascularity, the sensitivity and accuracy of CNB were higher than those of FNAC (91.0% vs. 88.7%, 91.0% vs. 84.8%, 92.8% vs. 85.1%; 93.2% vs. 88.8%, 91.7% vs. 84.8%, 93.3% vs. 85.2%), with statistically significant differences except for calcified nodules (all P<0.05). For the diagnosis of avascular nodules, the sensitivity and accuracy of FNAC were higher than those of CNB (92.7% vs. 90.2%, P=0.004; 96.2% vs. 90.5%, P=0.005).Conclusion CNB and FNAC have similar diagnostic efficacy for thyroid nodules with a diameter ≤2.0 cm, but CNB has certain advantages in distinguishing follicular tumors. CNB is more effective than FNAC for thyroid nodules with a diameter >2.0 cm, calcified nodules with rich vascularity, and cystic or solid nodules. Combining FNAC and CNB examinations for nodules with the above characteristics can improve the preoperative diagnostic accuracy of thyroid nodules to a certain extent.