The paper introduces Multi-Platform Analysis (MPA) for the seismic performance of a structure controlled by Magneto-Rheological (MR) dampers and presents analytical assessment of the effect of MR damper when taking into account nonlinear behavior of the structure. This paper introduces the MR Damper Plugin that can facilitate communication between MATLAB/Simulink and a finite element analysis tool in order to account for more complex inelastic behavior of the structure with MR dampers. The MPA method using the developed MR Damper Plugin is validated with experimental results from the real-time hybrid simulation. By utilizing the proposed MPA method, the three-story RC structure controlled by MR dampers is more realistically modeled and its performance under seismic loads is investigated. It is concluded that MR damper designed for a linear structure is not effective in a nonlinear structure and can overestimate the effect of MR damper. This work is expected to overcome difficulties in the analytical assessment of structural control strategies for complex and nonlinear structures by obtaining more reliable results.