The invention belongs to the nuclear power station instrument control system technology field and especially relates to an instrument control system parameter setting method based on an FPGA and an apparatus thereof, wherein the method and the apparatus can be used to reduce FPGA resource consumption. The FPGA is connected to an upper computer. The method comprises the following steps that the FPGA reads a parameter in a memory connected to the FPGA; if the parameter is successfully read, the FPGA sets on-line operation parameters one by one; and if the on-line operation parameters are set one by one successfully, the upper computer arranges the corresponding parameter in the memory again according to the read on-line operation parameters which are set one by one and rewrites the parameter in the memory. The corresponding parameter in the memory is rearranged through the upper computer connected to the FPGA so that hardware resource consumption of the FPGA during a parameter setting process can be reduced.