The present invention relates to a method for preparing a modified conjugated diene-based polymer, and more particularly, provides a method for preparing a modified conjugated diene-based polymer including a step of polymerizing a conjugated diene-based monomer in the presence of an organometal compound in a hydrocarbon solvent to prepare an active polymer which is coupled with an organometal (Sl); and a step of reacting or coupling the active polymer prepared in step (Sl) with a modifier (S2), wherein step (Sl) is continuously performed in two or more polymerization reactors, and a polymerization conversion ratio in a first reactor among the polymerization reactors is 50% or less.