The introduction of new types of heat exchangers with phase transitions and the solution of problems of optimizing the design and operational characteristics are a priority within the framework of the energy saving program. Known methods for calculating the heat-hydrodynamic parameters of the flow of refrigerants often do not take into account the specifics of boiling processes at low temperatures as well as in channels with a small flow area. This paper presents the results of modeling heat transfer during the boiling of refrigerants in the channels of evaporators of heat and cold energy complexes, taking into account the true flow parameters. The proposed mathematical model of the boiling of the working substance in channels of various shapes is based on the true flow parameters which imply knowledge of the channel cross-sectional areas occupied by each of the phases. The value of the true volumetric steam content provides the most correct modeling of two-phase flows in a wide range of regime and geometric parameters. The paper uses the equations of material and heat balance in combination with the equation of heat transfer from the environment to the boiling refrigerant. The map of flow regimes is used as an empirical component. A program has been developed for calculating the proposed system of equations which is solved iteratively at each time step using the finite volume method. Comparison of calculation results with experimental data on models of round and rectangular channels with intracanal boiling of refrigerants at positive and negative saturation temperatures is performed. It is shown that the calculation error does not exceed 10 % for a round and 20 % for a rectangular flow section. The verification results showed the possibility of using the model in the framework of engineering calculations. The proposed mathematical model can be used as the basis for the calculation programs for existing evaporators and for the creation of new types of heat exchangers with in-tube boiling of the working substance. The proposed method allows optimizing both geometric and thermal-hydrodynamic parameters.