Disclosed are a method for producing a modified conjugated diene polymer improved in quality stability, more enhanced in low heat buildup and reinforcing ability when used in a rubber composition, excellent in wear resistance, mechanical characteristics and processability, and improved in cold flow; and a rubber composition using the same. The method includes a step of modifying an active end of an active end-containing conjugated diene polymer having a cis-1,4-bond content of 75% or more with an alkoxysilane compound containing at least one functional group selected from the group consisting of (a) an epoxy group, (b) an isocyanate group and (c) a carboxyl group, and a step of adding a condensation accelerator to conduct condensation reaction of the alkoxysilane compound (residue) in an aqueous solution having a pH of 9 to 14 and a temperature of 85 to 180° C.