There have been some software tools of managing references when researchers prepare for their research publications, such as zotero and endnote. During last several years, developers of these kinds of tools tried to design a new feature or interface that can be used to visualize the “reference relations” between scientific articles. However, probably because of the complexity of formatting reference data and the data inconsistency between different data sources, it seems that only a few existing tools have implemented similar but limited feature. In this study, we compared different graph algorithms and selected the most appropriate one to model and further implement the reference network. We also designed and implemented a reference mapping software which could demonstrate the relation network between scientific publications. A detailed evaluation on the tool was also provided.