Abstract: The beam control system is the nerve center of the high power phased array antenna, responsible for precise control and condition monitoring of all the cell phases in the antenna array. In order to solve the need of online updating or maintenance of control system, a remote updating system based on SoPC is constructed. A reconfigurable method of remote online updating for FPGA hardware configuration file and Nios II software program file is proposed. The boot sequence copying hardware configuration code and software code is analyzed, and the advanced BootLoader is carried out to specify boot address of the application mode image manually. The EPCS device stores a factory pattern image for remote updates and multiple application pattern images for antenna phase control. The CAN communication bus and custom CAN application layer protocols are used to transmit data and verify data, ensuring the reliability and efficiency of the transmission. The experiment verifies the feasibility of the scheme and the system can switch between multiple configuration programs. Even if the remote update fails, the FPGA can automatically load the factory mode image to ensure the system is safe and reliable. The system is simple, and the method is flexible.