Water conservation in mining is the key to solving the conflict between coal resource exploitation and ecological environment protection, especially in arid and semi-arid mining areas. Continuous excavation and continuous backfilling (CECB) in longwall mining is an important method to realize water conservation mining. Considering the different boundary conditions of the main roof stress in different mining phases, the mechanical models of clamped–clamped beam, continuous beam, and elastic foundation beam among filling body, main roof, and strata are established. Furthermore, the spatio-temporal evolution mechanisms of mining-induced fractures (MIF) are studied. It is found that there is a hyperbolic function relationship between MIF and the mining roadway (MR) filling percentages. Based on mining the XV coal seam under CECB in the Wangtaipu Coal Mine, the distribution patterns of MIF are studied. It is concluded that the distribution pattern is an isosceles trapezoid with the moving angle of overlying strata as the bottom angle, and the upper and lower boundary of MIF as the two parallel sides. Based on the influence coefficient of MR filling percentages on MIF, the curve of the MIF height is divided into three ranges, which include the stability control range, the critical range, and the lost control range. The controlling effects of MR filling percentages are studied, and the calculation expression of the MIF height in the stability control range is given. In engineering practice, 90% MR filling percentage is used for CECB. The MIF height is about 3.0 times of mining height, and the main roof beam is not broken. The water-resisting property of aquiclude III is not destroyed, thus, the mining does not adversely impact the water. The results provide theories and practices for controlling MIF under CECB in the conditions of extremely close distance aquifers.