A method of manufacturing a semiconductor structure includes receiving a substrate; patterning a first active region, a second active region and an isolation between the first active region and the second active region over the substrate; disposing an inter-level dielectric (ILD) over the substrate; forming a first gate extended over the first active region, the isolation and the second active region; and forming a second gate over the first active region and the second active region, wherein the second gate includes a first section disposed over the first active region and a second section disposed over the second active region, a portion of the ILD is disposed between the first section and the second section.