This paper presents the results of mathematical modeling of the water-in-oil emulsion dynamics under the thermal influence taking into account the thermal convection within the emulsion system. Two cases of thermal influence on the water-in-oil emulsion are considered: microwave impact and contact heating. Dimensionless parameters (Rayleigh, Ostrogradsky and Archimedes numbers) characterizing the state of the system are introduced. Numerical calculations of the emulsion system dynamics for various values of dimensionless parameters are carried out. Calculations showed that thermal convection occurs in the emulsion system. At the same time, thermal convection leads not only to distortion of isotherms, but it can also have a negative effect on the process of stratification of the water-in-oil emulsion. It is found that when critical values of Rayleigh and Ostrogradsky numbers are reached, both the character of the convective flows in the liquid and the sedimentation intensity of the emulsion drops change. Based on the results of multiparametric calculations, diagrams of the total emulsion stratification are constructed at the presence of thermal convection in a fluid. The diagram allows to estimate the possibility of stratification of the emulsion system under thermal exposure.