The process of two-phase filtration in a carbonate formation of fractured-pore type is considered. A mathematical model in a spatially two-dimensional formulation is proposed, a numerical method for solution and a parallel algorithm for its implementation are developed. The mathematical model is based on the Buckley-Leverett approach. The reservoir takes into account the exchange of fluids between low-permeability pores and natural fracturing, specified within the framework of the dual porosity model. The numerical algorithm is based on the use of the finite difference method and the splitting scheme by physical processes. To speed up calculations, a parallel algorithm based on two-dimensional domain decomposition is used. Numerical experiments were carried out, which showed that the developed algorithm is highly efficient and allows one to calculate the necessary characteristics of the modeled physical process.