The invention discloses a system for updating an FPGA (Field Programmable Gate Array) configuration program from a long distance based on the control of a processor and a method for updating the FPGA configuration program from a long distance based on the control of the processor. The system comprises a processor module, an FPGA module, an SPI (Serial Peripheral Interface) memory module and a buffer module, wherein the processor module is connected with the SPI memory module and is connected with a communication interface, the SPI memory module is connected with the FPGA module, and the processor module is connected with the SPI memory module by the buffer module. When the configuration program of an FPGA requires to be updated, an upper computer or a terminal downloads the FPGA configuration program into the SPI memory module through the communication interface and the processor module, and the FPGA module can automatically load the configuration program memorized in the SPI memory module in a MasterSPI mode. According to the system and the method, the FPGA configuration program is updated from a long distance, the function of updating the configuration program on line under the non-outage situation is realized, and therefore, the system and the method are particularly suitable for on-site application.