In this paper, a probabilistic analysis is implemented to determine the settlement of immersed tunnel elements and the effects of subsoil stiffness variability. A soil-structure interaction model is used to study the effects of subsoil stiffness on the shear behavior of tunnel joints. Site investigation data is obtained from the Hongkong-Zhuhai-Macau Bridge (HZMB) Tunnel project in China. Two probabilistic methods, the Point Estimate Method and Monte Carlo simulation, are compared when determining the tunnel settlements. The first is computationally more efficient and has sufficient accuracy, while the latter is extremely accurate with higher computational costs. Based on the settlement results, spatial variability of the soil stiffness is quantitatively assessed. The soil-structure interaction analysis and derivation of shear forces in tunnel joints is performed by coupling FE analysis to a Monte-Carlo model. The results show that tunnel structure behavior is significantly influenced by the soil parameters uncertainty.