This paper proposed a universal method for implementing PTP (Precision Time Protocol) for test systems with the 1000M Ethernet Interface. To achieve the synchronization accuracy of sub-microsecond, the configurable real-time clock and the time stamp module were realized in the programmable logic which makes the PHY and MAC to be free of time stamp functions in the communication link. PTPd (Precision Time Protocol deamon, an open source implementation) was modified and transplanted into the embedded Linux system to realize PTP state machine while the IEEE 1588 IP core device driver was developed to provide the application layer with access to the accurate time-stamp obtained in link layer by IEEE 1588 IP core. This project structure makes the transplantation process concentrate on the time adjustment algorithm design in the application layer regardless of obtaining a precise time stamp in the hardware. The proposed method was evaluated on the Xilinx Zynq-7000 SOC platform by outputting PPS (Pulse Per Second) which can verify the synchronization accuracy of all nodes (master and slaves) in the network. After quantifying the accuracy and stability of the synchronization offset, we concluded that clock frequency offset and network transmission delay are the main influence factors for synchronization and proved the feasibility of maintaining submicrosecond-level synchronization accuracy within multi-level switch topology.