The invention discloses a device and a method for synchronizing system frequency in a packet transport network, and relates to a packet transport network in optical communication. The system frequency synchronizing device comprises a microcomputer processor, a field programmable gate array (FPGA) processing module, a clock integrated circuit, a packet transport network service disk, a synchronous state byte extracting module, a synchronous state byte generating module, a phase locked loop circuit, an external clock input circuit, a high stable crystal oscillator, a clock distributing circuit, a HDB3 coding module and an external clock output circuit, wherein the FPGA processing module comprises a preceding stage preselector, a priority level control module, a first selector, a second selector and a third selector. By the device and method, the system frequency in the whole packet transport network can be synchronized rapidly, data business package transmission and smooth transition can be carried out rapidly and hierarchically, and the device is flexible and has high reliability.