This paper analyzes the limitations of point-to-point data transmission interconnected parallel bus in the current smart substation system. PCI Express high-speed serial interface technology has been proposed to achieve point-to-point Ethernet data transmission. The design applies the architecture of Spartan-6 XC6SLX45T FPGA, and takes full advantage of FPGA parallel data processing features and extensive IP resource, to achieve a high-bandwidth and high reliability of multi-channel Ethernet point-to-point data transmission. It is greatly enhances the smart substation system performance.