The invention provides a waveguide micro-nanometer machining system and method. The waveguide micro-nanometer machining system and method are low in machining cost, high in precision and good in consistency. The waveguide micro-nanometer machining system is characterized by, comprising, a light source portion, a machining portion, a multi-freedom-degree workbench, an optical platform, a blowing portion, a suction portion and a control portion, wherein the light source portion provides laser beams, the machining portion focuses the laser beams on a substrate for photolithography machining and monitors the machining process in real time, the machining portion is provided with a variable-focus lens, a three-dimensional morphology instrument, a camera and a temperature measuring instrument, the multi-freedom-degree workbench drives the substrate to move in multiple freedom degree directions according to a preset waveguide pattern, the optical platform is used for installation of the multi-freedom-degree workbench and isolates external vibration, the blowing portion is arranged on one side of the multi-freedom-degree workbench and conducts blowing towards a machining area, the suction portion is arranged on the other side of the multi-freedom-degree workbench and conducting suction and removal on the gas blown by the blowing portion, and the control portion is connected with the light source portion, the machining portion, the multi-freedom-degree workbench, the optical platform, the blowing portion and the suction portion and controls operation of the light source portion, the machining portion, the multi-freedom-degree workbench, the optical platform, the blowing portion and the suction portion.