With the vigorous development of industrial automation and the Internet of things, the transmission of data is more dependent on immediacy, so network devices have higher and higher requirements for time synchronization accuracy. The clock source of common network devices is provided by the transistor oscillator in the server, but the oscillator will change with factors such as aging and temperature, and it cannot be guaranteed that the oscillator in the server will work at the same frequency. Time synchronization can be achieved by technologies such as IRIG-B, NTP, or IEEE 1588 (PTP), but the hardware cost of building IRIG-B is high, and NTP has the lowest cost, but it can only provide time accuracy from milliseconds to microseconds. PTP can provide sub-microsecond or even nanosecond time precision. It is a system of time synchronization mechanisms through Ethernet transmission. In this article, we first propose a time synchronization system using the development board and PDP protocol. On the Xilinx Zynq-7000 SOC platform of Petalinux, we implement the hardware solution of Linux PTP. The hardware time stamp is 20 ns. To improve the accuracy, the congenital frequency error between the oscillators must be considered. Therefore, a PTP auxiliary time stamp with dynamic frequency compensation is proposed and designed into a chip. Experimental results show that at 45 nm (TN40G) it can operate at 370 MHz and achieve 2.7 ns resolution, which can be applied to more demands.