The study of three-phase fluid filtration in the pore space is one of the urgent tasks in the development of oil and gas and gas condensate fields. In the study of three-phase flows, semi-empirical methods for calculating relative phase permeabilities (RPP) are used in practice, which do not consider the structure of the pore space and the fundamental equations of hydrodynamics. The paper proposes and substantiates a physical and mathematical model of mass transfer in the filtration flow of an oil-water-gas mixture in a porous medium. The pore space structure model is based on the distribution of pore diameters obtained from capillary pressure curves (CCP). In the core, clusters are identified, consisting of a large channel through which oil, water and gas move in a “beaded” mode; channels of medium diameter filled with water and gas and channels of small radius in which gas moves. A system of equations is presented and solved that determines the distribution of moving volumes and volumetric flows over channels and phases. When determining pressure losses in the system of pore channels, friction losses, local losses, and also losses due to interfacial interaction are taken into account. For the first time, on the basis of a hydrodynamic model, analytical expressions were obtained to determine the RPP for oil, water and gas. The calculation-experimental method is based on three model experiments, the results of which determine the properties of the cluster channels in relation to the separately filtered phases. It is shown that the developed theory and calculation method, in the particular case of an oil-water mixture, coincide with the previously developed theory of two-phase filtration on the core scale.