A new process of fabricating microstructures through micro electrochemical milling (micro EC milling) is proposed. By utilizing side wall of simple micro tool electrode rotating at high speed like micro mechanical milling and controlling the movement track on NC three-axis feed worktable, microstructures with high precision can be milled by micro-ECM under high-frequency short-pulse current. Micro EC milling can greatly improve the machining status in the tiny machining gap and thus make machining stable by simple rotary column electrode. The influence factors on the accuracy of micro-EC milling were investigated through process experiments, such as feed speed, machining voltage and kind of electrolyte. The process of the NC generating micro-ECM integrating CAD/CAM technology is studied. G code for machining complex microstructures can be generated by the universal CAD/CAM of traditional milling based on UG software. Last, Microstructures with complex shape were milled by this process, for example the micro bend beam with width of about 50μm, and its aspect ratio is about 6.