A modified conjugated diene-based polymer, a method of making the same, and a rubber composition including the same are disclosed herein. The modified conjugated diene-based polymer has excellent processability and good tensile strength and viscoelasticity. In some embodiments, a modified conjugated diene-based polymer includes a first chain including a repeating unit derived from a conjugated diene-based monomer, a second chain including a repeating unit derived from a compound represented by Formula 1 or Formula 2, and a derived unit from an alkoxysilane-based modifier, wherein the first chain and the second chain are coupled by the derived unit from the modifier.