An FPGA-based interface signal remapping method, relates to the technical field of nuclear power system, and solves the technical problems of poor reliability, readability and debuggability in the prior art. The method comprises dividing an internal programmable logic of an FPGA chip into two independent modules, with one module being an I/O module and the other module being a Core module, using the I/O module to process signal excursion occurring when an external signal is input to or output from the FPGA chip, signal collision caused by line multiplexing, metastable state in a data transmission process, and a data transmission error between asynchronous clock domains, using the Core module to implement logical processing and computing; and introducing a master clock signal outside the FPGA chip into the FPGA chip through a global clock pin of the FPGA chip. The method provided in the invention is suitable for a nuclear power protection system platform.