To　target　the　problems　of　performance,　cost　and　energy　consumption　in　large　scale　communications　of　high　performance　computing,　a　hybrid　hierarchical　topology　and　corresponding　partitioning　approach　are　proposed　in　this　paper.　The　proposed　hierarchical　topology　taking　full　advantages　of　both　traditional　metallic　lines　and　emerging　interconnections　to　implement　one-hop　local　direct　communication　within　the　cluster　and　one-hop　global　high-speed　communication　between　clusters.　The　customized　interconnection　topology　can　be　designed　according　different　applications　through　the　proposed　partitioning　approach　to　get　a　better　trade-off　between　performance　and　cost.　The　case　study　proved　that　the　partitioning　approach　can　implement　the　fast　mapping　from　the　design　to　real　high　performance　computing　system　with　multi-FPGAs,　and　accelerate　the　realization　of　high　performance　reconfigurable　computing　systems.　©　2014　WIT　Press.