We have developed an open-type magnetically shielded room composed of magnetic square cylinders that has been used for an actual MRI in a hospital. To improve shielding performance, we propose here a method to control the path of the magnetic flux in the wall composed of the magnetic square cylinders by changing the magnetic permeability in each direction of the square cylinders spatially. First, we discuss a method to control the magnetic permeability in each direction of the square cylinders independently by inserting slits without changing the outside dimensions of the square cylinders, by using 3-D magnetic field analysis. Then, the effectiveness of the design of controlling the flux pass was shown by magnetic field analysis and experiments.