This paper implements a lightweight workflow engine system which is flexible and can be configured. The system uses tools of JaWE for visual modeling, then it generats XPDL format process definition file. It designs an engine executive mechanism based on Token, which makes the control of engine system with the business process implementation more accurate and efficient. It adopts appropriate process definition management strategy that gives the modification definition support during process operation. At the same time, the engine forms business system by using the way based on components configuration, which makes application engine business system have great flexibility. The engine system has been successfully applied in a pharmaceutical enterprise project management platform, and has obtained a good application effect.