Abstract: Current space exploration activities have become increasingly frequent, particularly organic molecules in space exploration is an important task. Due to the special working conditions in space, the general merchandise mass spectrometer can’t meet the requirements such as volume, power consumption and analysis ability. So this need to research and development a mass spectrometer with compact size, low power consumption and high stability. In this study, a new type square ion trap formed multiple circular electrode was put forward base on the principle of ion trap. Such polycyclic pressure structure can effectively reduce the volume of the ion trap, so as to realize the miniaturization of mass spectrometer instrument. Power supply by using DC voltage of the composition ratio sub-period, the detection of mass spectrometer was expanded successfully. Through the simulation calculation, the relationship of ion oscillation frequency and its mass number was fitted. The mass resolution of the mass spectrometer is greater than 1400 for the mass number from 1 to 2000 u, which can meet the basic requirement of high molecular mass resolution.