As the main form of new urbanization, the coordinated development of cities in metropolitan areas requires reliable and efficient rail transit skeleton support. However, in the rapid development of metropolitan areas, the layout and analysis of multi-level rail transit systems have a certain lag. Taking the Xi’an metropolitan area as an example, this study analyzes the comprehensive accessibility and resilience of the multi-level rail transit network, and proposes an expansion plan accordingly. The traffic analysis zone (TAZ) is divided by towns and streets, and the relationship between points of interest (POIs) and the regional average level is analyzed using DEA. The improved weighted average travel time model is built with the analysis results as regional weights; a site selection model based on multiple construction influencing factors is proposed, and four expansion plans, namely, economic optimal, environmental optimal, transport optimal, and comprehensive optimal, are designed. The peak passenger flow scenario and the “failure–reparation” scenario during the entire operation period are designed to analyze the resilience of four plans, and the resilience is quantified by the elasticity curve of the maximum connected subgraph ratio (MCSR) changing over time. The research results show that the transport optimal plan has the best comprehensive accessibility and resilience, reducing travel costs in Houzhenzi Town, which has the worst accessibility, by 34%. The expansion model and evaluation method in this study can provide an empirical example for the development of other metropolitan areas and provide a reasonable benchmark and guidance for the development of multi-level rail transit networks in future urban areas.