The study of resistance coefficient for permeable tetrahedron frames (PTF) with seepage effect is of practical significance. PTF were taken as large-scale roughness in this research. Using the penetration depth, a two-layer dynamic model was established for the turbulent flow over large-scale roughness. The flow was divided into two layers, the permeable layer and the free-flow layer, along the water depth. Considering roughness area and seepage effect in the bottom, the resistance equation was derived with this two-layer model. Flume experiments of PTF were conducted and results present that the vertical distribution of longitudinal velocity is S-shaped when frames are laid. The key parameter, shape factor, was calibrated by 47 sets of data with the Reynolds number ranging from 25,000 to 50,000.