Micro-milling technology is one of the most suitable micro-machining techniques for processing high aspect ratio microstructures, but the tools limit its development. In view of micro-milling of high aspect ratio microstructure, a new PCD miller was proposed with large length-diameter ratio and straight edges. The influence of tool structure on milling force and burr height was studied by Deform finite element simulation. Furthermore, the multi-objective response surface methodology is used to test three factors, namely the side edge clearance (SEC), the bottom edge clearance (BEC) and the bottom edge inclination angle (BEIA). Finally, the optimized structural parameters of micro-milling tool are obtained, which are SEC 30°, BEC 15°, BEIA 7°.