It is important of rock crack fine test for deep rock engineering. The high frequency part of Nyquist diagram of rock electrochemical impedance spectroscopy reflects the rock volume change characteristics, which can express the change information of rock internal cracks. With the topological theory, the topological characteristics of Nyquist diagram of sandstone, mudstone and granite are researched. The results show that the electrochemical impedance spectroscopy diagrams which come from the same size sample using the uniform test are isomorphism, and which can express using the same function. It shows the rock electrochemical process is regularity. At the same time, topological separation of rock electrochemical impedance spectroscopy diagram is researched. Fine change of rock crack can be detected with topological separation.