Provided is a technique for comprehensively understanding the relationship between brain regions. A brain connectivity analysis system herein includes a memory configured to have stored therein a connectivity analysis program for analyzing the connectivity; and a processor configured to read the connectivity analysis program from the memory and analyze the connectivity. The processor is configured to execute a process of acquiring from a storage unit measured data on a plurality of selected regions of a brain, a process of determining at least two of the plurality of regions as seed regions and calculating a plurality of connectivity features for the seed regions and other regions from the measured data on the plurality of regions, and a process of generating a connectivity feature graph showing a relationship between a transfer delay time and another connectivity feature of each region that are included in the plurality of connectivity features.