A multi-frequency time-division multiplexing tapered laser amplification control system is developed. By controlling the output frequency and working time sequence of seed laser, the system can realize laser amplification in three different modes including high isolation single frequency, proportion adjustable dual-frequencies, and composite multi-frequency modulation. Optical characteristics of the control system are investigated experimentally. Results show that extinction ratio between the output linear polarization laser beam is 30 dB, and the switching time between different working modes is 100 ns. The proposed system can improve the utilization efficiency of lasers, which is suitable for the fields with higher requirements for output power and integration of laser, such as atom interferometer based precision measurement physics and atom interferometer application technology.