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With the rapid growth of high performance embedded processing requirements in the test information processing field, embedded single-core systems based on FPGA are now gradually exposing the shortages such as high power consumption, poor parallelism and so on. To solve these problems, a design methodology of embedded dual-core systems with Xilinx Virtex-5 series FPGA was proposed. An overall architecture of dual-core embedded system was built. The key techniques including data-exchange and synchronization between dual-core, configuration storage and auto boosting were well designed. The experiments on the Virtex-5 ML510 development board demonstrate the rationality and correctness of the proposed methodology. Meanwhile, the effective design methodology can provide reliable reference for other dual-core embedded system based on FPGA.