Hierarchical network operation and resource control system and method for a mega satellite constellation, belonging to the field of spatial information technology, are provided. The hierarchical network operation and resource control system includes a service layer, a global organization layer, a local coordination layer and a resource layer. The service layer is used as an input to drive operation of whole system. The global organization layer is to realize “operation, measurement and control” integrated control and decision of whole network. The local coordination layer is to realize local management decision and management slice generation. The resource layer is to provide physical resource and physical device and realize resource virtualization. By deploying local coordination layer controllers on GSO or MEO satellites, the deployment of local coordination layer controllers is not limited by inability of deploying ground stations globally and therefore the control of large-scale LEO satellite constellation can be achieved.