The complex geological structure of Taiwan often makes it difficult to control the deformation behavior of tunnel excavations. To simplify analyses, most traditional empirical formulations and modern numerical analyses do not consider the existence of rock bolts. For this reason, this study aimed to investigate the vertical displacements caused in tunnel crowns under various geological conditions using a three-dimensional finite element analysis with tunnels of different cross sections as an example. The analysis was performed using two rock material models: the Mohr–Coulomb and Hoek–Brown models. The results indicated that there was an insignificant difference between the two models in terms of the magnitudes of displacement and the distribution profiles obtained. When a tunnel was being excavated, the weaker the site was geologically and the larger the cross section, the larger the vertical crown displacement. In addition, the presence of rock bolts had a significant influence on the displacement in areas where the geology was weak and the cross section was large. The numerical analysis results of the Mohr–Coulomb and Hoek–Brown models were compared with the values calculated using the formulas suggested by Unlu and Gercek. At the excavation face, the displacement ratio derived from the prediction formula of Unlu and Gercek was smaller than the numerical analysis result, and the difference between the two became larger when the rock mass quality was worse.