Eccentric structures will have torsional vibrations subjected to earthquakes, which can accelerate the damage of structures, and even become the main cause of building collapse. Semi-active control systems equipped with multiple magnetorheological (MR) dampers have been widely applied in structural vibration control. In this study, numerical models of spatial eccentric structures with multiple MR dampers were established, and time history analysis was conducted to mitigate torsional vibrations of eccentric structures. Firstly, a full-scale spatial eccentric structure model with both plan asymmetry and vertical irregularity was established in OpenSEES, and the accuracy of the structure model was verified by comparisons with model results from SAP2000. Then, the mathematical model of MR dampers was introduced to the structure model using the ‘Truss’ element and self-defined material in OpenSEES, and damping forces obtained from the MR damper model were compared with experimental data. Finally, modal analysis and nonlinear time history analysis of the eccentric structure model equipped with multiple MR dampers subjected to different seismic excitations were performed. Comparisons between the seismic responses of the uncontrolled structure and the structure with multiple MR dampers were carried out to demonstrate the effectiveness of the MR control system. Numerical results show that the control system with multiple MR dampers can significantly attenuate the torsional vibrations of eccentric structures, and thus possess significant engineering application prospects.