Since numerical simulation method came out, it has caused a great importance to tunnel engineers and has been used widely. But it has been restricted in three-dimensional numerical analysis of multi-element and multi-working conditions because the out of memory of personal computer, the high cost of high-performance computer and so on. In view of this, we need to search the low-cost computing devices to solve the large-scale three-dimensional numerical simulation in tunnel engineering. After investigation and study, we have built a Linux-based PC cluster system successfully, and use it to simulate the excavation process of Xiamen Jiaheyuan underground access which is a rectangular shallow buried soft soil tunnel. The simulation results provide a basis for the construction. Linux-based PC cluster system provides a convenient and cheap solution for tunnel engineers in three-dimensional numerical simulation of multi-element and multi-working conditions.