Given the wide distribution of carbonate pillars in the Three Gorges reservoir area, there is a need to investigate the possible structural damage they experience from long-term water-level fluctuations. This study analysed the coupled effects of an improved time-dependent crack propagation pattern and failure modes of structural rock masses under stress-seepage using the Jianchuandong pillar hazardous rock mass (JCD) as a case study. A new crack simulation method based on FLAC 3D is proposed in which the interface element is immediately set on the surface of the yielding zone during the calculation step when a zone yields under tensile or shear stress. The two zones are directly separated during the tension or shearing of the bond at the contact surface. The JCD simulations illustrated that fractures and failure zones within the rock mass would propagate along the existing vertical cracks and extend to the base toe. The base rock mass would experience fracturing, finally leading to failure of the entire rock mass. The presented model provides sufficiently accurate predictions and is a suitable method for analysing time-dependent failure of pillar hazardous rock masses subject to water-level fluctuations. Thematic collection: This article is part of the Role of water in destabilizing slopes collection available at: https://www.lyellcollection.org/cc/Role-of-water-in-destabilizing-slopes