The present application discloses a method for manufacturing semiconductor devices having gate dielectric layers at different thickness. The gate dielectric layers having other than the minimum thickness are respectively formed by the following steps: step 1: forming a first mask layer; step 2: etching the first mask layer to form a first opening; step 3: etching a semiconductor substrate at the bottom of the first opening to form a second groove; step 4: filling the second groove and the first opening with the second material layer; step 5: etching back the second material layer to form the gate dielectric layer, such that the second material layer is flush with the top surface of the semiconductor substrate; and step 6: removing the first mask layer.