A method of pulse electrochemical machining in discrete fields and domains was introduced to solve the problems in microchannel arrays machining on difficult-to-cut metal surface. This method has the characteristics of processing microchannels with high surface quality and a non-penetrating structure. The machining zone of each channel was separated by the specially designed fence-like template made of nonconductive material, and hence the electrolyte flow field and electric field are confined and improved, because of which a higher process stability and good machining accuracy and consistency can be achieved. Both simulation analysis and experiments verified the effectiveness of the method. The distributions of flow field and electrical field of this method are better than those of the through-mask Electrochemical Machining (ECM) method and electrochemical pattern transfer method. Nine channels with a 538.76 μm width, 25.78 μm depth, and an overcut of 19.38 μm are obtained within 1 min. Single-factor experiments were conducted and the results show that good process performance can be obtained with a short machining time, low voltage amplitude, low duty cycle, and high pulse frequency. Thus, the presented method of pulse EMC in discrete fields and domains is suitable for mass production of non-penetrating microstructures with the advantages of high efficiency, high quality, and low cost.