Embodiments of the present invention disclose a packet synchronization method and system of an intelligent substation process layer network, wherein the method includes: recording transmission delay on a network transmission device in a sampled value (SV) packet sent by a merging unit; and implementing, by a SV data receiving device, packet synchronization according to the transmission delay on the network transmission device recorded in the SV packet, so as to achieve that the SV data receiving device synchronizes received packets of different merging units, and accordingly ensure that the SV data receiving device can correctly perform data calculation and actions. Such a method can solve the problem that the current process layer network relies too much on a time synchronization network.