A network node, a communication system, and a method for transmitting a clock packet through a tunnel are disclosed. The method includes: encapsulating a tunnel ingress clock packet received at an ingress of a tunnel in an encapsulation mode corresponding to the tunnel, and performing clock correction for the encapsulated clock packet; and sending the corrected clock packet to an egress of the tunnel. The network node for processing a clock packet includes an encapsulating module and a sending module. The communication system includes the network node for processing a clock packet, and further includes an intra-tunnel network node and a tunnel egress network node. According to the present invention, a clock packet is re-encapsulated and transmitted through a tunnel. In the subsequent process of transmitting the clock packet transparently, the node itself serves as a clock reference point, and all network nodes do not need to synchronize time absolutely.