Ceramic-copper substrates, as high-power, load-bearing components, are widely used in new energy vehicles, electric locomotives, high-energy lasers, integrated circuits, and other fields. The service length will depend on the substrate’s copper-coated surface quality, which frequently achieved by utilising an abrasive strip polishing procedure on the substrate’s copper-coated surface. Precision diamond fly-cutting processing machine tools were made because of the low processing accuracy and inability to match the production line’s efficiency. An analysis of the fly-cutting machining principle and the structural makeup of the ceramic-copper substrate is the first step in creating a roughness prediction model based on a tool tip trajectory. This model demonstrates that a shift in the tool tip trajectory due to spindle runout error directly impacts the machined surface’s roughness. The device’s structural optimisation design is derived from the above analyses and implemented using finite element software. Modal and harmonic response analysis validated the machine’s gantry symmetrical structural layout, a parametric variable optimisation design optimised the machine tool’s overall dimensions, and simulation validated the fly-cutterring’s constituent parts. Enhancing the machine tool’s stability and motion accuracy requires using the LK-G5000 laser sensor to measure the guideway’s straightness. The result verified the machine tool’s design index, with the Z- and Y-axes’ straightness being better than 2.42 μm/800 mm and 2.32 μm/200 mm, respectively. Ultimately, the device’s machining accuracy was confirmed. Experiments with flying-cut machining on a 190 × 140 mm ceramic-copper substrate yielded a roughness of Sa9.058 nm. According to the experimental results, the developed machine tool can fulfil the design specifications.