This paper develops an array micro-grooves manufacturing method using micro electrochemical machining (ECM) with disk electrode, which is prepared by in-situ micro wire electrical discharge machining (WEDM). This technology focuses on the difficulty of array structure manufacture in micro-electro-mechanical systems (MEMS). A micro-ECM system is built based on the micro-WEDM machine to achieve high precision processing of the array micro-grooves. Since micro-WEDM has good performance in high precision machining of the rotating structure, single and multi-edge disk electrodes can be fabricated in-situ using graphite. The as-prepared disk tool electrode is directly used for micro-electrochemical milling of the array micro-grooves without disassembling away from the device, which avoids the positioning error caused by the re-clamping of the disk electrode. With the advantages of high surface quality and no electrode loss, micro-ECM improves the manufacture performance of the micro-parts. Through wire path optimization, the shape accuracy of the disk edge is improved. After the research of the micro-ECM parameters, the process is improved, and finally, the high precision array micro-grooves are obtained. This method combines the advantages of micro-WEDM and disk electrode micro-ECM milling, and it is convenient for large-scale manufacture of array micro-structures on micro-parts and MEMS.