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FDK is the most popular algorithm used to reconstruct 3D image in cone beam CT system. To speed up the culculation, the paper analyses the properties of FDK, and realizes the backprojection part of the arithmetic on FPGA utilizing virtex5 1×110. The paper designs an eight parallel paths system which can processes eight paths dataflow simultaneously. The experiment result shows that the backproject culculation can be speeddup remarkably.The system can run 252 times faster than software do.