Disclosed are a method of preparing a modified conjugated diene-based polymer, a modified conjugated diene-based polymer prepared thereby, a rubber composition including the modified conjugated diene-based polymer, and a tire including the rubber composition. The method of preparing the modified conjugated diene-based polymer includes (a) polymerizing a vinyl aromatic monomer and a conjugated diene monomer through continuous solution polymerization using a multifunctional anionic polymerization initiator in the presence of a hydrocarbon solvent, thus forming an active polymer having a reactive end; and (b) coupling or linking the reactive end of the active polymer with an alkylamino alkoxy silane compound.