Objective To investigate the histological origin, diagnosis, differential diagnosis and treatment of thyroid carcinoma showing thymus-like differentiation (CASTLE). Methods Five patients with thyroid CASTLE were adopted by surgical resection and postoperative radiotherapy, and the CD5, CD117, CK5/6, P63, thyroid transcription factor-1 (TTF-1), carcino-embryonic antigen (CEA), calcitonin (CT), Ki-67, chromogranin A (CgA), thyrobolulin (Tg), peroxisome proliferator activated receptorγ (PPAR-γ), sodium iodide symporter (NIS), and thyroid stimulating hormone receptor (TSHR) were detected in tumor tissues by immunohistochemistry S-P method and v-raf murine sarcoma viral oncogene homolog B1 (BRAF)V600E gene and telomerase reverse transcriptase (TERT) promoter mutations were detected by DNA sequencing. Eight cases of poorly differentiated thyroid carcinoma and 6 cases of anaplastic thyroid carcinoma were adopted by comprehensive comparative analysis. Results Thyroid CASTLE tumor cells showed the positive expression of CD5, CD117, CK5/6 and P63, and the negative expression of TTF-1, CT, CgA, Tg, PPAR-γ, NIS and TSHR. There were partly positive expression for CK5/6, P63, TTF-1, CgA, Tg, NIS and TSHR, and negative expression for CD5 and CD117 in the poorly differentiated thyroid carcinoma and anaplastic thyroid carcinoma. The BRAFV600E gene and TERT promoter mutations were not detected in thyroid CASTLE, and the BRAFV600E gene mutations were also not detected in the poorly differentiated thyroid carcinoma and anaplastic thyroid carcinoma. Four cases of poorly differentiated thyroid carcinoma showed the TERT promoter mutations (4/8) included 3 cases with C228T and 1 case with C250T. Two cases of anaplastic thyroid carcinoma showed the TERT promoter mutations (2/6) included 1 case with C228T and 1 case with C250T. There was no recurrence and metastasis after 3–47 months (an average of 25.6 months) of followed-up in thyroid CASTLE patients. Conclusions The histological origin of thyroid CASTLE may be not related to the thyroid. There is important clinical value to combined detection of CD5, CD117, P63, TTF-1, Tg, NIS, and TSHR for the diagnosis and differential diagnosis of thyroid CASTLE. The further study still need for the diagnosis and differential diagnosis of thyroid CASTLE according to the detection of BRAFV600E and TERT promoter mutations.