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Research and development of sample wheel control system are one of the key technologies in atomic force microscopy (AFM) of deep space exploration. Small size, light weight and low power consumption are realized in modular design at the electric control system of Sample wheel. Using the AVR ATmega16 processor, the module communicates with the industrial motherboard of AFM scanner through the RS232 self-defined communication protocol. Open circuit and software design framework make a convenient interface for upgrading. The results from test institution show that the control system is full-featured, stable. It implements well in every control measure.