Abstract: In order to reduce the influence of vibrations caused by large shaking table testing to machine tools and precision instruments, etc. in shaking table laboratory and surrounding structures and improve the comfort of the people inside the structures, a frequency dependent and semi-active controlled three-dimensional (3D) floor isolation system was established. An on-off control method was proposed based on the dominant frequency of the input acceleration obtained by an online frequency detection method. Shaking table tests were conducted with vibrations caused by sinusoidal and earthquake type shakings. The test results show that the online frequency detection method can quickly and effectively detect the dominant frequency of the input motion, and the semi-active control can effectively reduce the floor vibrations with the detected frequency information. To improve the control efficiency in practice, the damping of the MR damper in the low damping force mode should be controlled as low as possible.