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The study of human brain functional network has been an important subject of biology in recent decades. As an important method of data analysis, visualization tools play a significant role in the study of brain science. However, the existing visualization tools of brain functional network have some problems, such as low information acquisition efficiency and single function. To solve the above problems, a visual analysis system was designed and implemented for comparing weighted graphs of brain network connections to help researchers explore the differences between different groups. A new visualization method for the comparison of weighted graphs of brain network is proposed and used for the first time. The user evaluation of this method shows that the new visualization method is more effective in the task of contrast analysis. In addition, the system combines data mining with visualization to enhance the presentation of differences among groups. Moreover, it provides a series of interactive ways such as multi-view collaboration for researchers to explore independently. Finally, two sets of public data sets are used for case analysis to verify the usefulness and efficiency of the system.