A method of manufacturing a semiconductor device having a self-aligned gate structure includes: providing at least one channel structure above at least one substrate; depositing at least one gate masking layer on the at least one channel structure so that the at least one gate masking layer is formed on top and side surfaces of the at least one channel structure and spread outward above the at least one substrate to form outer-extended portions of the at least one gate masking layer, before a gate-cut process is performed, wherein the at least one gate masking layer is self-aligned with respect to the at least one channel structure by the depositing; and removing the outer-extended portions of the at least one gate masking layer so that the at least one gate masking layer at both sides of the at least one channel structure has a same width.