Due to the flexible manufacturing systems cost too much money in the early stage of investment, and it works under the uncertainly making environment after implementing. Therefore, a business must estimate its benefit in detail and plan its best deployment before adopting the system. The results of plan often relations business working well or badly. These years, the flexible manufacturing system develops fast. There are many types of the flexible manufacturing system. The big scale, for example, flexible manufacturing line. And the small scale, for example, flexible manufacturing Module. For this reason, in order to take actions that suit different types of the estimation and to make a comprehensive survey of every kind of visible and invisible causes. This research plans to apply in the fuzzy theory, analytic hierarchy process, and multiple criteria decision making to implement the DSS of flexible manufacturing system allocation planning. The output of DSS can be the referenced the material purchasing agent.