The invention provides an ion source digital PID control parameter self-setting system and method. The system comprises an anode current measuring module, an anode high-voltage pulse generation module, a heater current control module, a heater current measuring module, an MCU master control module and a host computer. The anode current measuring module, the anode high-voltage pulse generation module, the heater current control module and the heater current measuring module are respectively connected with the MCU master control module. According to the invention, after a neutron pipe is replaced for the whole system, readjustment of digital PID control parameters is unnecessary, such that the problem of tedious and time-consuming manual debugging of the digital PID control parameters can be effectively solved, and at the same time, the requirement for debugging experience of debugging personnel is reduced.