Factory automation (FA) is a direct result of the underlying communication systems. To integrate the FA information and make FA control systems with flexibility and interoperability in automated manufacturing systems, the manufacturing message specification (MMS), Web services’ (WSs) technologies and typical FA systems are analyzed. A new design approach of the communication system structure is presented for FA systems in this paper. A prototype of FA control systems is used for evaluating performance of the communication system structure in C++ Visual Studio.NET and Java Borland Builder 9.0 development environment. The experimental results show that the proposed design approach is valid and promising.