In micro electrical discharge machining (micro-EDM) of deep holes, the debris dispersed in gap may increase the possibility of secondary discharge, resulting in electrode shape changing and low accuracy of machined hole. In this paper, the debris movement caused by flow fluid in the machining gap is analyzed to understand the mechanism of debris transport by using software, FLUENT. Comparison of debris movement calculated by the modified N-S equation and N-S equation is conducted. Debris movement calculated by the modified N-S equation is demonstrated to be correct by experiment. The simulation results can explain the phenomena such as subulate electrode and hole, unstable machining process and low machining speed in micro-EDM of deep holes. It is helpful to improve the process of micro-EDM.