AP1000 nuclear power plant has an advanced passive cooling system with a vast water tank located above the shield building, which may affect the seismic performance of the structure. This paper conducts a fragility assessment of shield building and considers the fluid-structure interaction (FSI) effect on the damage of the shield building. Arbitrary Lagrangian Eulerian algorithm is applied to calculate the FSI and eight cases of water levels are considered. Three different fragility analysis methods, namely linear regression, quadratic regression and truncated maximum likelihood estimation, are adopted for assessing the seismic vulnerability of shield building. It is indicated from the results that the regression and the truncated maximum likelihood estimation are close to each other. The maximum likelihood estimation not only can effectively save the computational cost, but also can assure the reasonable calculated results. It is observed that different water levels have the individual probabilities of failure, and case 6 has the smallest probability of failure with a more considerable seismic reduction, whereas the case 1 and case 2 have the higher failure probabilities. The fragility analysis framework can thus be applied for evaluating the vulnerability of shield building under earthquakes considering the FSI effect.