Fault is one of the most important factors affecting tunnel instability. As a significant and casual construction of Jinping II hydropower station, when the drain tunnel is excavated at depth of 1600 m, rockbursts and water inrush induced by several huge faults and zone of fracture have restricted the development of the whole construction. In this paper, a progressive failure progress numerical analysis code-RFPA (abbreviated from Rock Failure Process Analysis) is applied to investigate the influence of faults on tunnel instability and damaged zones. Numerical simulation is performed to analyze the stress distribution and wreck regions of the tunnel, and the results are consistent with the phenomena obtained from field observation. Moreover, the effects of fault characteristics and positions on the construction mechanical response are studied in details. Some distribution rules of surrounding rock stress of deep-buried tunnel are summarized to provide the reasonable references to TBM excavation and post-support of the drain tunnel, as well as the design and construction of similar engineering in future.