This paper introduces the design of a hyper parallel processing (HPP) controller, which is a system controller used in heterogeneous high performance computing systems. It connects several heterogeneous processors via HyperTransport (HT) interfaces, a commercial Infiniband HCA card with PCI-express interface, and a customized global synchronization network with self-defined high-speed interface. To accelerate intra-node communication and synchronization, global address space is supported and some dedicated hardware is integrated in the HPP controller to enable intra-node memory and shared I/O resources. On the prototype system with the HPP controller, evaluation results show that the proposed design achieves high communication efficiency, and obvious acceleration to synchronization operations.