The invention relates to a power source low-level all-digital amplitude phase control system for a high-energy particle accelerator and an implementation method thereof. The method comprises cooperation of signal preprocessing, digital signal processing and digital loop control. An analog circuit component of the signal preprocessing comprises six signal processing channels and one clock processing channel integrated on an analog part, wherein each signal processing channel comprises an attenuator, an amplifier and a filter; and the clock processing channel comprises an attenuator, an amplifier, a filter, a frequency multiplier and a frequency divider. A digital circuit component of the digital signal processing and the digital loop control comprises three A / D (Analog to Digital) converters for sampling six paths of signals, one D / A (Digital to Analog) converter for generating signals and one FPGA (Field Programmable Gate Array) for the digital signal processing and the digital loop control, wherein the three A / D converters, the D / A converter and the FPGA are integrated on a digital part. Through adoption of the power source low-level all-digital amplitude phase control system, the physical structural parameters of a super conduction cavity can be controlled, and high stability of the amplitude and phase of a super conduction cavity driving energy field can be kept.