A study has been carried out that effectively controls the vibration of asymmetric cable-stayed bridges caused by earthquakes with MR dampers. In order to enhance the practical serviceability of MR dampers, an asymmetric cable-stayed bridge structure has been designed and produced, and a MR damper has been produced so as to have this bridge structure controlled appropriately. An experiment that controls vertical and horizontal vibrations has been carried out by exciting the asymmetric cable-stayed bridge in the horizontal direction with the El-centro seismic wave. The control performance of the MR damper has been evaluated under the five control conditions in the experiments of vibration control in each direction. As a result of the experiment, MR dampers were proved to control vibrations more effectively when either Lyapunov control algorithm or Clipped-optimal control algorithm was used to control vibrations of the asymmetric cable-stayed bridge caused by earthquakes. In addition, different controlling effects were found in vibration controls in vertical and horizontal directions due to the asymmetry of the structure and the horizontal excitation. With such controlling effects, semi-active MR dampers are evaluated to effectively control vibrations caused by earthquakes in flexible and asymmetric structures such as asymmetric cable-stayed bridges.