With the micro-hole array structure more and more used in industrial areas, such as oil nozzle, spinneret and so on, its machining accuracy significantly affects the performance of the product. In the machining of micro-hole array by micro-EDM drilling, unavoidable tool electrode wear is one key factor affecting machining geometric and dimensional accuracy, and the effective energy of the discharge gap directly determines the amount of electrode wear. In present study, the characteristics of electrode wear and gap effective discharge energy were explored to meet the requirements of machining accuracy of micro-hole array machining. The effect of pulse generator parameters and electrode eccentric radius on electrode wear were concerned, and the electrode wear was reduced by optimizing pulse generator parameters and electrode eccentric radius. The geometry evolution rule of electrode was investigated, and the electrode wear model was established based on the electrode wear characteristic. The experimental result show that the electrode tip morphology tended to be stable and the axial wear of the tool electrode could be compensated evenly. In order to realize the accurate calculation of the gap effective discharge energy, a gap effective discharge energy detection system was built based on Lab VIEW. And the variation rule of gap effective discharge energy was obtained by micro-hole array machining experiment. In addition, the relationship between electrode wear and gap effective discharge energy was also studied in this paper. It was found that there was a parabolic relationship between electrode wear and effective energy before electrode wear was stable, and there was a linear relationship between them after electrode wear was stable.