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The conductivity of tracheid is closely related to the flow characteristics of water through the pit. The aim was to investigate flow resistance characteristics of border pits with different structures. The Bernoulli mathematical model of the torus-margo border pit was established based on the energy conservation law. According to the obtained mathematical model, the geometrical structures of pit, such as the pit diameter, aperture diameter, torus diameter, pore diameter and porosity of margo, were the main factors that affected the pit flow resistance characteristics. The flow through the pit was simulated with CFD software package Fluent 6.3, the pit margo was worked as porous medium, and the turbulent structure was modeled by low Re k—ε model. In the simulation, the influences of various pit structures on flow distribution in the pit were studied and analyzed. Resistance of pits were varied with morphology as predicted, the pit flow resistance was inversely proportional to pit diameter, aperture diameter, pit depth and margo pore size, and the pit flow resistance was proportional to torus size and margo thickness. The results supported the hypothesis of valve effect of the pit torus, when the distance between torus and center position was increased, pit flow resistance was decreased at the beginning,，and then it was increased, the pit flow resistance was increased with decrease of distance between margo and pit aperture. The research results provided theoretical basis for further study on the hydrodynamic characteristics of plant conduits.