The damage of the muscular system is one of the frequent complications in thyroid diseases, but today there is no unanimous view on the morphofunctional changes in masticatory muscles in hypothyroidism. The purpose of this study was to determine the peculiarities of the structural organization of the masseter and lateral pterygoid muscles of mature rats in various stages of experimentally modeled hypothyroidism. The study was performed on the masticatory muscles of mature male rats during the 14th, 21st, 28th days of the development of mercazolilum-induced hypothyroidism. The following research methods were used: injection method of study of the circulatory bed of the masticatory muscles; histological examination of blood vessels and tissue elements of the masticatory muscles; electron microscopic examination; morphometric analysis (mean value of blood vessels’ lumen and thickness of their walls; number of capillaries in 1 μm2 of cross section of muscular fiber; the quantity of the capillaries at one muscular fiber, the percentage of oxidative (OMF), oxidative-glycolytic (OGMF), glycolytic (GMF) muscular fibers, average muscular fiber area, biochemical methods, and statistical analysis was conducted out using the software RV.3.0. The development of hypothyroidism is indicated by the reduction of hormones of the thyroid gland in the blood. During the 14th day of the experiment in the arterial bed in the injection of Parisian blue in the masticatory muscles there is a deformation of the vascular pattern. The number of hemocapillaries decreases. The edema of the cytoplasm of endothelial cells is submicroscopically marked. In muscular fibers, the cross-striation is broken, the area of their cross-section is enlarged, the dilation and vacuolization are observed in the endomysium. A change was determined in the quantitative distribution of all types of fibers (the number of OGMF and OMF decreased, and the amount of GMF increased). At the ultramicroscopic level, there were observed pronounced changes in all types of muscular fibers, especially in the GMF and OMF of the masseter muscle. On the 21st day, a significant deformation of the vascular pattern was observed, with a decrease of the arterial lumen and an increase of the vein lumen. The number of hemocapillaries continues to decrease. Ultra-structurally, in the endothelial cells of the hemocapillaries of the masticatory muscles, edema changes progress. In muscular fibers there is a loss of cross-striation and observed swelling. There is a tendency to decrease of the number of OGMF and OMF and increase of the amount of GMF. At the ultramicroscopic level, there are pronounced changes in all types of fibers, especially in the masseter muscle. During the 28th day of mercazolilum-induced hypothyroidism changes in the vessels and muscle fibers are progressing. Described morphological changes are associated with the dynamics of the trace substances’ composition. Thus, in mercazolilum-induced hypothyroidism in the masticatory muscles there are edematous changes both in the vascular bed and in muscular fibers. Moreover, the changes are deepened depending on the duration of the experiment.