Disclosed are a method for preparing a conjugated diene polymer including synthesizing an initiator having an anionic end containing an amine and a cationic end containing an alkali metal, polymerizing a combination of an aromatic vinyl monomer using the initiator to synthesize a polymer having a modified end, coupling or reacting the polymer with a compound having at least one silyl group substituted by an alkoxy group and a nitrogen atom to prepare a modified conjugated diene polymer having one end containing amine and the other end containing silyl group substituted by one or more alkoxy group and a nitrogen atom, and a rubber composition comprising the conjugated diene polymer and silica as a reinforcing agent and thus exhibiting superior heat generation, tensile strength, abrasion resistance and wet skid resistance.