Water inrush from underlying aquifers under the synergistic action of complex faults and mining activities seriously threatens the mining of coal seams in North China. The failure characteristics of the coal seam floor under complex fault conditions are the keys to understanding the water inrush mechanism during mining. To investigate floor failure characteristics and water inrush mechanisms influenced by complex fault structures, theoretical analysis and numerical simulation were carried out. An improved theoretical model is first proposed, including complex fault structures such as horst, graben, and step fault structures. The calculation formula for waterproof coal pillars under complex fault conditions is established based on the improved theoretical model. The failure and displacement characteristics of the coal floor under complex faults are analyzed via numerical simulation. Compared with those under normal mining conditions, the theoretical and numerical simulation results reveal the following: (1) Under the horst structure, the floor failure characteristics show an increase in the compression failure area on both sides, and shear failure occurs on the large-dip fault side. The simulation results reveal that the failure width on the large-dip fault side increases by 25%, indicating a failure trend toward the large-dip fault side. The width of waterproof coal pillars needs to be increased by 20% to ensure mining safety. (2) Under the graben structure, the floor failure characteristics show an increase in the compression failure area on both sides, and shear failure occurs on the small-dip fault side. The simulation results reveal that the failure width on the small-dip fault side increases by 25%, indicating a failure trend toward the small-dip fault side. The width of waterproof coal pillars needs to be increased by 40% to ensure mining safety. (3) Under the step fault structure, the floor failure characteristics show compression failure on both sides, increasing the floor compression failure area on the large-dip fault side. The simulation results show that the failure width on the small-dip fault side increases by 15%, the large-dip fault side increases by 50%, and the floor failure depth increases by 20%. The width of waterproof coal pillars needs to be increased by 50% to ensure mining safety.