In order to study the risk response measures of subway crossing under the condition of complex building clusters, the overall three-dimensional spatial model of various interaction relationships (underpassing, side-passing, etc.) of subway crossing building clusters is established by establishing scientific and reasonable risk evaluation indicators, and the spatial interaction between subway structure and building clusters is comprehensively analyzed. The results show that targeted technical and management measures such as reasonable control of the distance between the subway structure and adjacent buildings, control of construction parameters, and reasonable arrangement of construction timing can effectively control risks and ensure project safety. The results can provide some reference for similar engineering applications.