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There are many problems in traditional network security and PC security protection systems, such as insecurity, inflexibility and so on, whether they are implemented by software or hardware. To solve the problems, this paper presents a reconfigurable security protection system on the basis of NetFPGA platform and embedded soft-core technology. This system consists of two subsystems, one is implemented on the NetFPGA for the subnet protection and the other is implemented on DE2 board to protect the terminal, in which NetFPGA is used to achieve packet filtering in hardware, immunity from ARP attacks in hardware, flow monitoring and transmitting with hardware acceleration, and DE2 board is used to realize AES/DES encryption modules in hardware. Moreover, the USB virus can be isolated effectively by the subsystem designed on DE2. To further enhance performance, security and flexibility of our system, including both the subnet protection subsystem and the terminal protection subsystem, we introduce two types of remote reconfigurable design method, by which administrator is able to reconfigure the two subsystems for both the software and the hardware logical circuits via any authorized devices. Extensive experiments show that all the functions of the blocks of the designed system are valid and the designed system is feasible.