Communication transmission in the near-Moon space is a critical enabler of scientific exploration in this region. However, the communication network in near-Moon space shows trends of diversification, heterogeneity, and collaboration, posing significant challenges to the management of an integrated communication network. This paper proposes a networking routing method for near-Moon-space cross-domain network transmission. Considering the constraints of heterogeneous networks including Moon–Earth, Moon–surface, and relay transmission, the method enhances transmission routing efficiency at the network layer of near-Moon-space systems, thereby improving the overall efficiency of heterogeneous network interactions. This research focuses on the networking routing of cross-domain networks. To simplify the research problem, a mixed link resource and scheduling model of heterogeneous networks is proposed. Based on this model, a time-varying and fixed topology network sub-network clustering method was designed to reduce the complexity of the routing algorithm. A routing scheduling algorithm is provided in combination with hierarchical routing search, and related experiments and comparisons were carried out. Finally, considering the practical issues of communication relay channels and rate limitations in relay satellites, time windows and communication rate constraints were used to enhance the reliability of the simulation validation. Simulation results show that this method effectively addresses the issue of low transmission interaction efficiency in heterogeneous networks within cislunar space. Compared with previous designs, it improves link load rate by 31%, reduces average service delay by 8%, and significantly enhances link stability and load rate.