The purpose of the present study is to develop a framework which can be used by researchers who are dealing with carbon dioxide flux data management and computing. Kepler, a scientific workflow system, was adopted as the tool of this framework. We used flux data collected from Chilan flux towers to test the framework. The result showed that Kepler system could be used to solve data management and computing issues such as complicate process of computing, the lack of software, time consuming on data handling and cleaning and real time data management. In addition, we chose the approach to use metadata as data content description and separate metadata from raw data storage. This approach indicated a useful tool kit in solving the archiving difficulty of the large volume of flux raw data, documentation of the whole calculation process and sharing the data and workflow through a distributed operation platform.