Abstract: Ultra-thick coal seams feature large stope spaces and extensive disturbance ranges. Significantly variable amplitude loading and unloading are prone to cause the fault rupture of floors of ultra-thick coal seams, inducing water disasters. Numerical simulation serves as a critical method for revealing the fault reactivation and water inrush mechanisms at the floors of ultra-thick coal seams. The key of this method is to accurately inflect the coupling characteristics of rock mass rupture and fissure water under significantly variable amplitude loading and unloading. This study determined the correlations of the damage variable with plastic strain and stress, deriving the equations for damage evolution of an intact rock mass under tensile/compressive loading and unloading. With the square tensile-shear stress and the Benzeggagh-Kenane fracture criteria as the criteria for initial, complete rock mass rupture, this study established the relationship between plastic displacement and strength deterioration, along with the constitutive relation of ductile fracturing under loading and unloading conditions. Then, using experimental data, this study built the shear constitutive relation of penetrating fractures under loading and unloading conditions. Based on fundamental equations and the equation of state, this study created the hydraulic simulation theory for fractured rock masses using the immersed boundary method. Finally, it developed a computational fluid dynamics-finite discrete element method (CFD-FDEM) coupled program to simulate the fault reactivation and water inrush processes at floors of ultra-thick coal seams. The results show that the CFD-FDEM coupled program can achieve both the numerical transformation of the faults at ultra-thick coal seams’ floors from a (quasi) continuous to discrete volume and the migration process of fissure water. The mining-induced damage of fault-bearing floors exhibited a W-shaped envelope, with the deepest part of damage located in a fault and its hanging walls (depth: 48.6 m) and the shallowest part of damage in the fault’s footwall (depth: 23 m). The faults at the stope floors and their hanging walls were subjected to significant advanced concentrated stress, which was then substantially unloaded in the goaf. This resulted in significant secondary failure in the goaf, leading to the formation of primary hydraulically conductive channels. The results of this study provide theoretical support for the prevention and control of water disasters at fault-bearing floors of ultra-thick coal seams.