In order to investigate the permeability anisotropy and stress-seepage coupling effect of the filled tube assemblage for geotube dams, a large-scale model experiment on stress-seepage coupling was used to study the effect of overburden pressure on the permeability and its anisotropy of the geotube assemblage under different arrangement modes. The experimental results show that the joints between geotubes are the main seepage channel of the assemblage. If the joints between geotubes are arranged parallel to the direction of seepage, the permeability coefficient of the assemblage is much larger than that of the vertical arrangement, and seepage damage is easy to occur. With the increase of the overburden stress, the permeability coefficient of the assembly decreases gradually and the anisotropy of permeability gradually increases. The influence of overburden pressure increase on permeability is different for different arrangement modes.