The invention discloses a high-voltage amplifier based on wireless data transmission isolation, and a control method thereof. The high-voltage amplifier comprises a main control processing unit and a plurality of auxiliary amplifier units; the main control processing unit comprises a main single-chip microcomputer, a main radio-frequency data transceiving module and a main power supply module; the main radio-frequency data transceiving module and the main power supply module are connected to the main single-chip microcomputer; the auxiliary amplifier units each comprise a slave radio-frequency data transceiving module, a signal conditioning and acquiring module, a slave single-chip microcomputer, a DDS waveform synthesis module, a filter module, a relay module, a same-phase / reverse-phase amplifier module and a slave power supply module; the slave radio-frequency data transceiving module, the signal conditioning and acquiring module, the relay module and the slave power supply module are connected with the slave single-chip microcomputer; and the slave single-chip microcomputer, the DDS waveform synthesis module, the filter module, the relay module and the same-phase / reverse-phase amplifier module are sequentially connected. By means of the high-voltage amplifier based on wireless data transmission isolation, and the control method thereof disclosed by the invention, the problem that the isolation voltage of an isolation amplifier is too low can be solved; and simultaneously, the amplifier waveform distortion problem based on the isolation amplifier or an optical coupler can be solved.