It is of great significance to assess the risk of building damage along the line that may be caused by metro tunnel construction. How to balance efficiency and accuracy is a challenge for risk assessment of tunnel underpass buildings. An improved three-stage building damage assessment method is proposed, in which the risk of tunnel underpass buildings is initially screened in the first two stages simultaneously from the perspective of both the hazard of tunnel excavation to the building and the vulnerability of the building itself, and a detailed multi-indicator assessment of the risk of tunnel underpass buildings is performed in the third stage. In the initial risk screening, Peck empirical formula and the ultimate tensile strain method are used to assess the hazard of tunnel excavation to the building, and the building integrity and the building, physical characteristics are used as the basis for building vulnerability assessment. In the detailed assessment of buildings damage risk, a three-dimensional finite element numerical model is established and multiple control indicators are selected to comprehensively assess the building damage risk caused by tunnel underpass. A shield tunnel underpass masonry building project is taken as an example to verify the rationality of the proposed method, and the results show that the introduction of vulnerability assessment as another basis for initial risk screening can effectively avoid underestimation of risk. The comparison of the assessment results with the measured shows that the improved three-stage method can accurately assess the risk of tunnel underpass buildings.