With the increasing capacity of the storage system and the speed of the SAR radar front-end data acquisition, the higher request of the performance of data transfer and storage system is put forward. A solution of high speed data transfer and storage system based on the PCI-E and the Aurora protocol using the hardware platform of Xilinx’s Virtex-5 series FPGA is proposed. Customizing a reliable frame format on the basis of Aurora protocol. Using the dual-port RAM for data cache and operating in ping-pang mode ensures the stability and reliability of the data transfer in the case of transfer speed mismatch of the input and output data. The transfer and storage system and PC via the PCI-E bus for communicating, command interaction using the PIO mode and image and list data transfer using the DMA mode. Actual test shows this solution can meet the request of a type of SAR radar system for high speed data transfer and storage.