The electrochemical machining technology has advantages of the machining performance. Due to the micro multiple tool is hard to design a flow channel system inside and cannot be rotated simultaneously, the metal oxides could not be removed from the machining gap effectively. Therefore, the through-mask assisted electrochemical machining of micro-hole arrays could not smoothly proceed. This study conduct ultrasonic vibrating assisted, magnetic field assisted, and ultrasonic vibration combined with magnetic field assisted through-mask electrochemical machining experiments by micro multiple tool electrodes. The experimental results show that the ultrasonic vibration combined with magnetic field assisted method has the best performance compared to other assisted methods. According to the experimental results, a shorter average diagonal length could be obtained by using ultrasonic vibration combined with magnetic field assisted method, and the quality of work-piece surface morphology was higher.