Optimization of thermochemical and biological transformations occurring during the heat treatment of food products can be carried out only taking into account the dynamics of the formation of temperature fields inside the processed products. A mathematical model of the Sous-Vide processing process has been developed, which provides the determination of the dynamics of changes in the temperature field of Sous-Vide processed functional food products based on animal and vegetable raw materials. To calculate the process of Sous-Vide processing of functional products, we used the differential equation of unsteady heat conduction taking into account the Bio criterion. When solving a system of partial differential equations, the mathematical package flexPDE is used. In calculations, a spatial grid with the number of nodes 20000 was used, the accuracy of calculations was 10E-4. Experimentally determined values of thermal conductivity, specific heat capacity, density and thermal diffusivity of each of the components of the food system are used in calculations. The results of the calculated experiment in mathematical modeling of the Sous-Vide processing process show the evolution of temperature fields in different sections of the food system and on its upper surface, having the shape of an ellipsoid of rotation. The dependences of the change in the thermophysical characteristics of the longitudinal and transverse flow of the food system coolant. The results of the computational experiment show a good convergence of the mathematical model and the results obtained, which is 94%, which indicates the adequacy of the developed mathematical model of the Sous-Vide processing process. The obtained mathematical model allows, by means of a computational experiment, to analyze and optimize the Sous-Vide processing modes of a wide range of food raw materials, of various geometric shapes and sizes, with different physicochemical and thermal properties, taking into account their non-stationarity under thermal influence.