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Researches on microscopic seepage mechanism and fine description of reservoir pore structure play an important role in effective development of low and ultralow permeability reservoir. The typical micro pore structure model was established by two ways of the conventional model reconstruction method and the built-in graphics function method of Comsol® in this paper. A pore scale flow simulation was conducted on the reconstructed model established by two different ways using creeping flow interface and Brinkman equation interface, respectively. The results showed that the simulation of the two models agreed well in the distribution of velocity, pressure, Reynolds number, and so on. And it verified the feasibility of the direct reconstruction method from graphic file to geometric model, which provided a new way for diversifying the numerical study of micro seepage mechanism.