In the era of network, B2B electronic commerce (EC) has become new bright spot and trend of future business development gradually. B2B electronic commerce has huge development potential in China. However, Chinese B2B market develops slowly. One of the important reasons is that coordinate control among organizations in B2B EC is complicated, and there exist seldom research on coordinate control among organizations in B2B EC in academia at present. Therefore, the paper analyses the structure of B2B EC, and describes various type organizations in B2B EC by agent. At last, the paper establishes model of coordinate control among organizations in B2B EC based on Multi-Agent system, and analyses the mechanism of coordinate control among organizations in B2B EC. That makes up the lack of existing research and provides basement to quantity and to manage harmonious control among organizations in B2B EC, and is conducive to the running of B2B EC smoothly in China.