The technique of planet occultation is one of the most effective methods in detecting Martian atmosphere and ionosphere. Changes in frequency, phase, amplitude and other physical quantities of radio signal from spacecraft, caused by passing through the atmosphere and ionosphere of the planet, were observed in rising and descending planet occultation events. The profiles of the atmosphere, density, temperature and pressure of the neutral atmosphere, and the electron density profile of the ionosphere can be obtained by using some inversion methods. In Chinese YH-1 Mars exploration mission, Earth-based planetary atmosphere occultation is an important scientific research assignment, and observation data arrangement is the first step of the inversion process. This paper presents the data processing of the Earth-based Martian atmosphere occultation processing system, and introduces the structure and function of the observation data arrangement module in detail, including time system transformation, ephemeris interpolation, coordinate system conversion, signal time delay correction and establishing occultation plane. Using our algorithm, some experimental results are generated by using data of MEX Radio Science from NASA Planetary Data System and data of MEX orbit, Earth and Mars ephemeris from MEX SPICE.