A method containing a step of reacting a conjugated diene polymer having an alkali metal or alkaline earth metal active end with a hydrocarbyloxysilane compound having one or more of each of the following functional groups I and II in its molecule to obtain a modified conjugated diene polymer containing a functional group II, and a step of mixing the modified conjugated diene polymer and a compound such as organic acid. A modified conjugated diene rubber which can be used as a raw material of a cross-linked rubber which can be used in tire treads and the like and can enhance low fuel consumption performance is provided. The functional group I is a hydrocarbyloxysilyl group. The functional group II is a nitrogen-containing group in which both of two hydrogen atoms of a primary amino group are substituted with protective groups.