The invention provides an FPGA-based digital wave-by-wave current limiting system which comprises the components of a current measurement circuit, an electric power electronic switch device, a switch device driving circuit, an analog conversion circuit, an AD conversion circuit and an FPGA chip, wherein switch device current which is detected by the current measurement circuit is converted to a signal which is suitable for acquisition of the AD conversion circuit through the analog conversion circuit. The signal is then converted to a digital signal by the AD conversion circuit. The FPGA chip acquires the digital signal, performs overcurrent judgment and outputs a pulse width signal duty ratio to the switch device driving circuit to the switch device driving circuit for driving the electric power electronic switch device. According to the FPGA-based digital wave-by-wave current limiting system, a digital method is utilized for realizing wave-by-wave current suppression; high operating speed of the FPGA can be realized, wherein the operating speed can reach dozens of MHz and relatively high calculating function is realized; and a more complicated algorithm and a high-efficiency fault tolerance mechanism can be added into the wave-by-wave current limiting function, so that the wave-by-wave current limiting system has higher flexibility, higher safety and higher reliability.