This study addresses problems of numerical methods for continuous media, such as the finite difference and finite element methods to simulate the discrete medium characteristics of a sandy cobble stratum. Based on the blockbased discrete element method, a discrete element model is built to simulate the process of shield tunneling through a sandy cobble stratum, and the displacement of joints and deformation of the surrounding rock and liner is studied. A finite difference model, in which a sandy cobble stratum is transformed into an equivalent continuous medium, is built to simulate the process of shield tunneling, and to compare the differences in simulation results between the discrete element model and the finite difference model. The results show that, in the discrete element model, the area at which the positive normal displacement of the joints exceeds 0.1 mm is primarily concentrated at the inverted arch, the area at which the negative normal displacement of the joints exceeds 0.1 mm is located at the hance, and the area at which the shear displacement of the joints exceeds 0.4 mm is primarily concentrated at the inverted arch. The simulation results of the discrete element method are greater than those of the finite difference method with respect to the deformation of the surrounding rock and liner; therefore, utilizing the discrete element method to verify the design of the tunnel and liner is relatively more secure and reasonable.