An advanced micro-hole electrical discharge machining (EDM) system with the adaptive fuzzy logic control and precision piezoelectric stage is developed in this study. A high-speed EDM monitoring system is implemented to measure the gap voltage, current, and ignition delay time, which are used to derive three input parameters, the average gap voltage, deviation of spark ratio, and change of deviation of spark ratio, for the fuzzy logic control. Servo displacement and speed of the piezoelectric stage during each data acquisition cycle are real-time synthesized by the adaptive fuzzy logic controller. Effects of the single and multiple input parameters, ignition delay threshold value, and maximum servo displacement and speed on the EDM drilling process are experimentally studied. Design of experiments (DOE) is applied to investigate the correlation of fuzzy logic control parameters. The optimal EDM parameter values are searched via the genetic algorithm. The optimal search result is experimentally validated. The fuzzy logic EDM control system has demonstrated the efficiency and stability in micro-hole drilling by reducing the frequency of irregular discharges and the drilling time.