BackgroundMicrocalcifications are suggested to be an indicator of thyroid malignancy, especially for papillary thyroid carcinoma (PTC), nonetheless, the association between macrocalcification and PTC is underexplored. Furthermore, screening methods like ultrasonography and ultrasound-guided fine needle aspiration biopsy (US-FNAB) are limited in evaluating macro-calcified thyroid nodules. Thus, we aimed to investigate the relationship between macrocalcification and PTC. We also explored the diagnostic efficiency of US-FNAB and proto-Oncogene Proteins B-raf V600E (BRAF V600E) mutation in macro-calcified thyroid nodules evaluation.MethodsA retrospective research of 2645 thyroid nodules from 2078 participants was performed and divided into three groups as non-, micro-, and macro-calcified for further PTC incidence comparison. Besides, a total of 100 macro-calcified thyroid nodules with both results of US-FNAB and BRAF V600E mutation were screened out for subsequent evaluation of diagnostic efficiency.ResultsCompared to non-calcification, macrocalcification showed a significantly higher incidence of PTC (31.5% vs. 23.2%,P<0.05). Additionally, when compared with a single US-FNAB, the combination of US-FNAB and BRAF V600E mutation showed better diagnostic efficiency in diagnosing macro-calcified thyroid nodule (area under the curve (AUC) 0.94 vs. 0.84,P=0.03), with a significantly higher sensitivity (100.0% vs. 67.2%,P<0.01) and a comparable standard of specificity (88.9% vs. 100.0%,P=0.13).ConclusionsOccurrence of macrocalcification in thyroid nodules may suggest a high risk of PTC, and the combination of US-FNAB and BRAF V600E showed a greater value in identifying macro-calcified thyroid nodules, especially with significantly higher sensitivity.Trial registrationThe Ethics Committee of The First Affiliated Hospital of Wenzhou Medical University (2018-026).Supplementary InformationThe online version contains supplementary material available at 10.1186/s12957-023-03016-7.