In this study, we examined the seismic isolation effects due to the difference between the center of mass of the building and the center of stiffness of isolation layer. Because the base isolation technique is a technique that is highly dependent on the performance of seismic isolation devices installed on the seismic isolation layer, we have to examine the horizontal stiffness of seismic isolation devices after making them. If difference between the design stiffness and the actual stiffness of the seismic isolation device occurred, a big problem may be generated in the upper members on the seismic isolation layer. The analytical results show that the more eccentricity increases, the more maximum response acceleration, story shear and the member forces of the upper part of the structure increases, and the damage is expected to be in excess. Therefore, it is recommended that if possible, isolation devices have to be designed to coincide the center of mass of the building with the center of stiffness of isolation layer. If not after making isolation devices, they need to be relocated to prevent the eccentricity.