Aim at the demand of analytical automation of sampling pretreatment, we designed an automatic sampling system which used ARM9 for microprocessor. The system designed in this paper is based on the processor of S3C2440 and the Windows CE operating system, and completed the work of programming in Visual Studio 2005. It uses stepping motors and precision pump as implementing agencies, and TA8435H as the stepping motor’s driver, uses LCD touch screen as human-computer interface. We accomplished software development in a customized Windows CE6.0 operating system. The paper mainly makes the detailed introduction to this system’s hardware platform design and software design based on WINCE embedded operation system.