Application of thermal ablation therapy by using microwave or radiofrequency energy for benign thyroid nodules or/ and thyroid malignancies gets increased world-wide. Potential risks involved in the ablation procedure are not uncommon and could be catastrophic when out of control. Ablation for pharyngeal esophageal diverticulum’s (PED) being misdiagnosed as thyroid nodules constitutes the risks. In this case report, the authors presented another potential threat to such ablation treatment, which derived from a trachea diverticulum complicated with inflammatory hyperplastic tissue by misdiagnosis as thyroid nodules. The tracheal diverticulum (TD) reported in this study was interpreted as a calcified thyroid nodule on ultrasonography at first, then microwave ablation (MWA) was accordingly recommended as one of the therapeutic options. However, the first author, experienced with the ultrasonic features of PED, insisted the differential diagnosis should be made between nodule and PED. Subsequently, swallow contrast-enhanced ultrasonography (CEUS) and barium meal test were carried out successively, but neither of them reported the presence of PED. Percutaneous fine-needle aspiration (FNA) was hence operated to identify pathological characteristics of the “calcified thyroid nodule”, and cytological tests under microscopy indicated the nodule originated from trachea due to the presence of ciliated columnar epithelial cells with inflammatory exudates within the specimen. Cervical and thoracic X-ray CT examination was further conducted, and a TD was discovered. The case was finally concluded as a TD with inflammatory hyperplastic tissue. The value of this case lies in that once a TD was misdiagnosed as ablation-candidate thyroid nodule in conventional ultrasonography could cause the latent danger to thyroid thermal therapy. Rigorous and effective differential diagnosis prior to thermal ablation procedure could prevent misdiagnosis and mistreatment.