The invention relates to a magnetically-controlled reactor control system which comprises a low-voltage part and a high-voltage part, wherein the low-voltage part comprises an upper industrial computer, an LCD touch screen, a main controller, a wireless communication master station and a relay protection device, and is used for detecting voltage and current signals, completing the control function via a control target and sending firing angle data to the high-voltage part in a wireless communication manner; and the high-voltage part comprises an excitation controller A, an excitation controller B and an excitation controller C, and is used for receiving the firing angle instruction sent out by the low-voltage part in a wireless communication manner, and uploading the fault information and control winding voltage to the main controller of the low-voltage part. The magnetically-controlled reactor control system is safe and reliable in insulation of high-voltage part and low-voltage part, is easy to implement, and reduces equipment cost and field construction workload; through synchronous signals provided by the control winding, control accuracy and stability are improved; and under the situation that a hardware platform is basically unchanged, requirements of various application occasions can be met through only selecting and assembling a small quantity of hardware and software modules.