In order to determine the safe width of fault waterproof coal (rock) pillar and solve the safety mining problem，the lower protective seam mining of a coal mine in Shanxi Province is taken as an engineering research object. Taking faults’ occurrence and throw into account，numerical tests with FLAC 3D numerical simulation software are conducted to investigate the development of mining-induced fractures in coal seam roof and floor，and the reasonable width of waterproof coal (rock) pillar is determinated through combining numerical simulation with empirical formula method. In addition，the risk evaluation of coal seam floor water inrush of No.6 mining area in this coal mine is finished using the result of numerical simulation. It is shown that fault is not only an important factor affecting the disturbance failure extent of coal seam floor in protective seam mining，but a key factor determining the safe width of waterproof coal (rock) pillar. In the risk evaluation of coal mine water inrush，the effect from mining-induced disturbance failure of coal seam floor should be considered.