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Most existing super peer based Peer-to-Peer (P2P) systems have only one level super peer, it can not support hierarchical P2P architecture, especially, the effectiveness, efficiency and scalability can not satisfy some application's requirements with the growth of the system. In this paper, we design a P2P system with hierarchical structure. First, we propose a Multi-Level Super Peer (MLSP) based P2P architecture for supporting hierarchical P2P system, where the upper level super peer summarizes its subordinates' meta information. Second, based on this architecture, we develop our query executing algorithm by only spreading query to the upper level super peer and flooding query between root level super peers. Finally, we design a protocol to handle the join and leave of peers, super peer selection, split and merge. By conducting experiments on a simulated large-scale network, we come to the conclusion that the effectiveness, efficiency and scalability improve prominently in the proposed system.