The present invention relates to a method for setting multilayer satellite network system route, including steps of: 1. setting parameters for the network initialization; 2. fixing a time, solving satellite orbit parameters in the interval of time, calculating the location coordinates of the satellite and the length of the link between stars, and establishing a network topological structure; 3. calculating the load of link between stars of the multi-layer satellite network; 4. calculating the process and exchange time delay on stars according to the queuing theory; 5. searching source satellite and object satellite of each satellite layer; 6. selecting the satellite layer for transporting services according to the communication service instruction requirement and network states, and searching an optimum route according to routing algorithm. Relative to traditional stationary orbit satellite, the present invention has small transmission delay, and high validity. The system has advantages of more flexible routing, effective guaranty of service quality, multiple replaceable chain circuits, stronger survivability, a capacity of processing and exchanging on star, optical or microwave links between stars, and capability of providing wideband synthetic service for users in global scope.