Objective To investigate the diagnostic causes of Bethesda Ⅲ (AUS/FLUS) thyroid nodules and the value of subcategories in predicting risk of malignancy (ROM) of thyroid nodules. Methods The data of 356 cases of Bethesda Ⅲ nodules were collected, and the causes, ROM and subcategories were summarized. Results In 97 resected specimens, 72 were diagnosed as papillary thyroid carcinoma (PTC), and the ROM of Bethesda Ⅲ was 74.2%. The main factors affecting the diagnosis of PTC were small lesions, few puncture cells, atypical nuclear features and lack of papillary structure. Secondary factors included significant interstitial fibrosis or calcification, unqualified smear, improper fixation, poor staining and lack of cytological diagnosis experience. According to the subcategories of Bethesda Ⅲ, 132 cases were included in low-risk group, nodules of 12 cases in the group were resected, which ROM was 8.3%; 122 cases were included in high-risk group, nodules of 70 cases were resected, which ROM was 92.9%; 102 cases were included in middle-risk group, nodules of 15 cases were resected, which ROM was 40.0%. The differences between high-risk group and low/medium-risk group were statistically significant (P＜0.05). Conclusion The diagnosis of Bethesda Ⅲ is subjective and empirical in some degree, and the risk related subcategories of Bethesda Ⅲ nodules is helpful to achieve better ROM stratification and improve the clinical management of the disease.