In this article, the effect of various factors, such as earthquake characteristics, base isolation system properties, and dynamic model of isolated structure, on the design of control algorithm of the semi-active base isolation systems composed of a magneto-rheological damper and a base isolation system is studied. The weighting parameters defined in the control algorithm are the design variables that are determined for various design objectives. For numerical simulation, a six-story base isolated shear frame has been subjected to different earthquakes while different values have been considered for the dynamic parameters of both base isolation system and isolated structure. The results show that to design the control algorithm proportionally with each design objective, an appropriate range to select the weighting parameter can be determined instead of a specific value, which these ranges are almost similar under different earthquake records. Hence, when the control algorithm is designed under an earthquake, the designed control algorithm satisfies the considered design objective under other earthquake records. Also, because the appropriate ranges to select the weighting parameter are independent of the dynamic properties of both the base isolation system and the isolated structure, the company that produces the magneto-rheological damper can propose the appropriate range for designing the weighting parameters of control algorithm which is compatible with both different structures and earthquakes.