Disclosed are an anionic polymerization initiator, which is an organo-alkali metal compound having an anionic end including an amine group, a method of preparing a modified conjugated diene-based polymer using the same, and a rubber composition including the modified conjugated diene-based polymer prepared thereby. Specifically the polydiene and the anionic initiator contain a group of Chemical Formula 8, below, in Chemical Formula 8, R1 and R2 are each independently a C1-C20 alkyl group, R3 is a C1-C10 alkylene group, R4 and R5 each independently a C1-C10 alkyl group, R1 and R2 are linked with each other to form a ring structure, and * represents a bonding position.