Abstract: Research on the theory and application of miniature mass spectrometer is very important in the field of space exploration. The commercial mass spectrometers have the disadvantages of large weight, large size, high energy consumption and complex realization principle, which are difficult to be applied in the field of space exploration. The small mass spectrometry detector of organic molecules in space was designed by using electrostatic double square ion trap and ion focusing technique. The detector consists of mass sensor, voltage control circuit and micro current detection amplifying circuit. The sensor has a cylindrical shape, and multiple ring electrodes with different potential are built in its cavity. Double square ion trap is formed in the axial direction of the cavity, and the ion can form stable oscillation in the potential well. Ion of different charge-mass ratio has different vibration frequency, and its vibration frequency is inversely proportional to the ion mass. Under the action of the extraction electrode, the signal generated by measuring the Faraday tube and vibration frequency is extracted by FFT. Thus the mass of organic molecules can be detected. In theory, the main technical indexes are as follows: mass range of m/z 1-2 000, resolution>400, sensitivity>100 cps/ppb, mass<4.5 kg, power<5 W, code rate>1.5 kbps. The feasibility of the technique is verified by the preliminary test results. In the later stage, the specific performance of the whole mass spectrometer will be tested by the study of the ion source and its combined with mass sensor.