A feature of mathematical modeling and study of a complex three-dimensional biomechanical object is the ability to achieve unity of geometric, physical, mechanical and biological indicators with the individual characteristics of the patient. A rather urgent problem of clinical dentistry is the development of recommendations on the distribution of masticatory pressure in patients with balanced occlusal-articulation relationships of the dentition. This paper considers one of the aspects of this problem associated with modeling the stress-strain state of the functional masticatory center, which is localized in the region of the first molars and the premolar groups of the upper and lower jaws during physiological occlusion. To determine the biomechanical parameters of the functional masticatory center, an analysis of the stress-strain state of mathematical models of this fragment of the dentition was carried out using the finite element method. When developing a model of a biomechanical system, the surrounding biological tissues were considered discretely in terms of structure and physical and mechanical properties: dentin, enamel, periodontium, bone, cement. A technique for analyzing models of the functional masticatory center is proposed, which makes it possible to establish the relationship between the magnitudes and directions of functional loads, as well as internal stresses and deformations. As a result of the analysis of the stress-strain state of geometric and finite element models, the distributions of maximum strains and stresses in a given section under the action of specified loads were obtained. It has been established that under the conditions of this mathematical model, the areas of the apical periodontium of the teeth have the maximum shock-absorbing properties, and the functional masticatory center is equated to a static system. The capabilities of modern computer software make it possible to expand the understanding of areas of stress concentration with varying load parameters in the functional masticatory center in order to determine the most “critical” zones in order to predict and prevent the development of long-term complications.