The workflow management system should be flexible enough to manage workflow changes caused by new partnerships, new technologies, and new strategies in collaborative design. Therefore, this paper attempts to introduce the version concept of configuration management into the workflow management system to handle this problem. In this study, the baseline is applied to record the sequence of tasks in a workflow and the version number of the baseline is given whenever the workflow is created. Whenever any change happens, the version number of the task or baseline will be modified accordingly. Both version numbers of the baseline and the tasks are checked while the workflow is being processed, so that the user could notice any differences in the tasks or workflow and decides whether to use the newly changed workflow or to keep the old version. A JADE development platform was applied to develop a prototype system and the architecture was based on Workflow Management Coalition. A scenario was shown in this paper to verify the feasibility of this study, and the result showed that users can choose whether to use the modified workflow baseline or not, for any running processes. This approach increases the workflow flexibility for collaborative design projects.