The invention provides a satellite interlayer topology refactoring method based on a discrete sub-topology sequence and a genetic algorithm. The method comprises the steps of S1, establishing a discrete sub-topology time sequence according to an inherent law of relative motion among satellites and representing an evolution process of a dynamic topology through the discrete sub-topology time sequence; S2, on the basis of a discrete sub-graph sequence, refactoring sides in all LEO/MEO (Low-earth Orbit/Middle-earth Orbit) satellite interlayer topologies, namely refactoring all interlayer inter-satellite links; and S3, carrying out optimization search on different refactoring results and obtaining an optical topology refactoring mode through utilization of the genetic algorithm. According to the method, a change process of a network topology in a system cycle can be expressed, the refactoring times of the established network topology is enabled to be as little as possible, and the refactoring cost is relatively low.