Elevated levels of total hardness in drinking water can readily result in scaling, which poses a threat to both the safety of water quality and the convenience of its use. While there is a wealth of research on the removal of calcium hardness, there is a dearth of studies focusing on the removal of magnesium hardness. In light of this, the present study employs modified induced crystallization softening (MICS) to delineate the removal pathways and mechanisms of magnesium hardness, and to investigate viable methods for its enhancement and application. Our research has determined that magnesium hardness can be effectively removed from water through the MICS, with the dosage of softening agents (NaOH) being a significant factor that influences this removal, whereas the fixed bed height within the fluidized bed exerts minimal impact on the process. In the low-dose stage (less than 250 mg/L), when the pH is below 10.0, up to 20% of magnesium hardness can be removed, predominantly through the crystallization of (Ca0.936Mg0.064)CO3. As the dosage increases to the moderate stage (250–400 mg/L), the conversion of excess bicarbonate (HCO3−) to carbonate (CO32−) in the water hinders further removal of magnesium hardness. In the high-dose stage (exceeding 400 mg/L), when the pH rises above 10.5, the removal rate of magnesium hardness can be enhanced to over 75%, with the crystallization of Mg(OH)2 being the primary removal mechanism. Density functional theory calculations, along with molecular dynamics simulations of cohesive energy and bond energy, substantiate the feasibility of the identified magnesium removal pathways. The addition of coagulants (FeCl3) and an decrease in the up-flow velocity can further augment the removal efficiency of magnesium hardness by promoting the crystallinity of Mg(OH)2 during the high-dose stage (exceeding 400 mg/L). In practical engineering applications, the strategic control of softening agent dosages enables the achievement of varying levels of magnesium hardness removal, tailored to specific water quality requirements.