In order to solve the difficulty and complexity for three-dimensional dynamic uncertainty problem of tunnel surrounding area. Based on the finite element method (FEM), this paper presents an efficient and accurate method for dynamic performance simulation of super long tunnel structure by using 2.5-dimension technique and PML to deal with the boundary truncated by FEM mesh. Since the combination of 2.5-dimension method, finite element method (FEM) and perfectly matched layer (PML) is not common, we derive the equations of the combination of 2.5D technique and FEM, and emphasize its compatibility with 2.5D technique and PML. After a brief introduction of the model, a series of verification examples are provided to prove the accuracy of the model. Finally, parametric studies are carried out to evaluate the influence of tunnel and soil properties on soil vibration. The results show that the proposed 2.5D MEF-PML method can solve the problem that the finite element method can not deal with the infinite domain, and has high accuracy, making it possible to accurately consider the influence of the factors around the tunnel in the dynamic analysis of the tunnel.