Servo scanning 3D micro electrical discharge machining (3D SSMEDM) is a novel and effective method in fabricating complex 3D micro structures with high aspect ratio on conducting materials. In 3D SSMEDM process, the axial wear of tool electrode can be compensated automatically by servo-keeping discharge gap, instead of the traditional methods that depend on experiential models or intermittent compensation. However, the effects of process parameters on 3D SSMEDM have not been reported up until now. In this study, the emphasis is laid on the effects of pulse duration, peak current, machining polarity, track style, track overlap, and scanning velocity on the 3D SSMEDM performances of machining efficiency, processing status, and surface accuracy. A series of experiments were carried out by machining a micro-rectangle cavity (900 μm×600 μm) on doped silicon. The experimental results were obtained as follows. Peak current plays a main role in machining efficiency and surface accuracy. Pulse duration affects obviously the stability of discharge state. The material removal rate of cathode processing is about 3/5 of that of anode processing. Compared with direction-parallel path, contour-parallel path is better in counteracting the lateral wear of tool electrode end. Scanning velocity should be selected moderately to avoid electric arc and short. Track overlap should be slightly less than the radius of tool electrode. In addition, a typical 3D micro structure of eye shape was machined based on the optimized process parameters. These results are beneficial to improve machining stability, accuracy, and efficiency in 3D SSMEDM.