The present invention provides a modified conjugated diene-based polymer which includes a functional group derived from a substituted styrene-based compound and a functional group derived from an aminosilane-based compound, a method for preparing the same, and a rubber composition including the same. The modified conjugated diene-based polymer includes the functional group derived from an aminosilane-based compound of Formula 1 and a functional group derived from a substituted styrene-based compound of Formula 2 at both terminals of a main chain, and thus, shows a high modification ratio. When applying the polymer in a rubber composition, excellent affinity with a filler may be shown, and as a result, agglomeration of a filler in the rubber composition may be prevented, and the dispersibility of the filler may be increased, thereby improving the processability of the rubber composition.