Abstract: This paper is based on Xilinx high speed serial protocol to communicate matching.For the differences between Virtex-5 GTX and Virtex-6 GTH should made on pre-emphasis value, reception equalization values, receiving terminal voltage and differential voltage transmission values, so as to adapt to the data communication between GTX and GTH.The actual communication parameters are measured by IBERT GTX/GTH transceiver, and add the clock calibration module to shield the receiver due to differences in clock phase offset, greatly improving the stability of data transmission.Experimental results show that: Virtex-5 GTX and Virtex-6 GTH serial transceivers data error rate of 10^-12 or less, the single lane speed reaches 2.5 Gb/s, the total transmission speed of sixteen lanes reaches 40 Gb/s.