The invention provides an operating system clock synchronization method and a system under a 2oo3 redundancy structure, which is characterized in that the system comprises the following steps: a delayobtaining step: each node in a node network is communicated with other nodes in the node network once, and the communication delay of each node and other nodes in the node network is obtained; According to the communication delay between each node and the rest nodes, the average communication delay between each node and the rest nodes is calculated, a node with the smallest average communicationdelay is selected as the master clock node, and the rest nodes in the node network are taken as the slave clock nodes. Node synchronization step: a synchronization network is established to synchronize the slave clock node and the master clock node. The clock synchronization network established by the invention can cover a 2oo3 redundant structure, can independently maintain each node in the network, and can carry out operations such as adding, deleting nodes or links, etc. It can be adjusted according to different network load and physical structure.