Tohoku University and Hokkaido University completed the development of 50-kg microsatellite RISING-2 for earth observation in 2011. It has a telescope with 5-m resolution, total 8 image sensors, and wheel-based attitude control system, for the observation missions of multi-spectrum cumulonimbus clouds and terrestrial lightning events such as sprite. The launch opportunity has not been decided yet, so the improvement of onboard codes for FPGA and CPU are being continued at this time. This paper shows the development method of command and data handling system (C&DH) based on the actual experience for the project RISING-2 and project RAIKO. This method and experience are expected to contribute for the development of future micro and nano satellites.