A micro-EDM equipment which can fabricate three-dimensional micro-structures is developed. A method of electrode wear compensation on-line which is very important to micro 3D structures machined by micro-EDM is presented. In this method, the wear of electrode can be predicted by the statistics law of open rate of discharge status, therefore, its precise model which is very difficult to build as well as the special CAD/CAM system is hardly necessary. At the same time, the micro-EDM CAD/CAM technology which applies the universal CAD/CAM software for milling is also researched and experienced on Unigraphics (UG). At last, micro 3D structures, a micro hemisphere with diameter ∅150+m and a micro 3D beam which is very popular in MEMS, are machined on silicon wafer by this way, which proves the wide useful of this method and the promising application in MEMS.