Increasing evidence indicates that cancer stem cells (CSCs) are initiators of the occurrence, development, and recurrence of malignant tumors. Mitochondria are important organelles in eukaryotic cells, not only responsible for converting part of energy released during nutrients oxidation into the energy-yielding molecule adenosine triphosphate (ATP) to fuel the activities of cell, but also play essential roles in processes such as cell apoptosis and cellular proliferation. The mitochondrial-related abnormalities have also been considered to have an important role in the origin and development of tumors. This study aimed at testing the abnormalities in mitochondrial function and energy/metabolism-related phenotypes in thyroid cancer stem cells (TCSCs). TCSCs were isolated and identified from MDA-T32 thyroid carcinoma cell line. The mitochondrial mass and mitochondrial arrangement, amount of mitochondrial DNA (mtDNA), mitochondrial membrane potential (MMP), oxygen/glucose consumption, and intracellular concentrations of reactive oxygen species (ROS) and ATP levels were examined. Perinuclear mitochondrial distribution, low amount of mtDNA and oxygen/glucose consumption, high MMP, and low intracellular ROS and ATP concentrations were observed in TCSCs. Alterations in mitochondrial function and cellular energy metabolism may be used as novel indicators of thyroid cancer.