Disclosed are a method of preparing a modified conjugated diene-based polymer, a modified conjugated diene-based polymer prepared thereby, and a rubber composition and a tire, including the modified conjugated diene-based polymer. The method of preparing the modified conjugated diene-based polymer includes (a) polymerizing a vinyl aromatic monomer and a conjugated diene monomer using an organo-alkali metal compound in the presence of a hydrocarbon solvent, thus forming an active polymer having an alkali metal end and (b) coupling or linking the active polymer having the alkali metal end with a compound represented by Chemical Formula 1.