Objective To investigate the diagnostic significance of fine needle aspiration cytology (FNAC) combined with BRAFV600E gene detection in the diagnosis of cervical lymph node metastasis of thyroid cancer. Methods Atotal of 140 patients with suspected cervical lymph node metastasis of thyroid cancer were collected as the research objects, and all patients were given ultrasound-guided FNAC and detection of BRAFV600E gene. The significance of the diagnosis was analyzed according to the gold standard after pathological examination. Results All the 140 patients underwent surgical treatment. For FNAC, the sensitivity was 63.6% (84/132), the specificity was 100% (8/8), the accuracy was 65.7% (92/140), the positive predictive value was 100% (84/84), and the negative predictive value was 14.3% (8/56). For detection of BRAFV600E gene, the sensitivity was 84.8% (112/132), the specificity was 100% (8/8), the accuracy was 85.7% (120/140), the positive predictive value was 100% (112/112), and the negative predictive value was 28.5% (8/28). For FNAC combined with BRAFV600E gene detection, the sensitivity was 90.9% (120/132), the specificity was 100% (8/8), the accuracy was 91.4% (128/140), the positive predictive value was 100% (120/120), and the negative predictive value was 40.0% (8/20). The area under curve of receiver operating characteristic for FNAC, detection of BRAFV600E gene, and FNAC combined with BRAFV600E gene detection were 0.818, 0.924, and 0.955, respectively. Conclusion FNAC combine with BRAFV600E gene detection improves the accuracy of neck lymph node metastasis in patients with thyroid cancer, which is worthyof performed.