This article analyses the model of the ATM-PON system and its downstream data structure. Based on the analysis, the layout design of ONT's physical layers is illustrated, including some important key technique, such as cell delineating, DSS, and the VHDL programming technique of FPGA, and so on. Then the implementation of the physical layer and the timing relationship of synchronization is given to prove that the design destination of the physical layer of ONT is accomplished successfully.