A method and system for realizing a FPGA server, wherein centralized monitoring and managing all SoC FPGA compute nodes within the server by a motherboard, the motherboard comprising: a plurality of self-defined management interfaces for connecting the SoC FPGA compute nodes to supply power and data switch to the SoC FPGA compute nodes; a management network switch module for interconnecting the SoC FPGA compute nodes and supplying management; and a core control unit for managing the SoC FPGA compute nodes through the self-defined management interfaces and a self-defined management interface protocol, and acquiring operating parameters of the SoC FPGA compute nodes to manage and monitor the SoC FPGA compute nodes based on the management interface protocol.