The invention relates to a microscale pulse electrolysis jet processing system and a processing method thereof, which belongs to the technical field of electrolysis processing. The microscale pulse electrolysis jet processing system comprises a pulse direct-current power supply, an electrolyte jet injection device, an electrolyte circulating and filtering system, a workpiece installing and fixing system and a worktable motion control system, wherein a filter core body and a nozzle are arranged in the electrolyte jet injection device, are made of metal materials, thereby not only increasing filter effect and eliminating an electrolyte pulsation phenomenon, but also leading the electrolyte to be sufficiently polarized negatively under the function of a high-voltage pulse direct-current electric field and then to transmitted to a position to be processed of a processing workpiece in a high-speed flowing mode, electrochemical anode dissolution is generated at the injection point, the high-quality and efficient processing of microstructures such as small holes, narrow grooves, dimpling pits, and the like are realized by using the numerical control motion of a machine tool worktable.