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In order to download different bitstream files to automation test system FPGA without interrupting it’s normal operation, a new dynamic partial reconfiguration technology is introduced and a CPCI TT C transponder automation test system is developed based on it. The system master computer software can download partial reconfiguration bitstream files which can realize different test functions to FPGA by PCI bus, when the system is running. The test result shows that many traditional cards can be replaced by a card with partial reconfiguration technology in this automation test system. The system has higher integration, lower hardware price, more design flexibility and online upgrading function.