A semiconductor structure includes a semiconductor substrate including a first active region and a chop region. The semiconductor structure also includes a source/drain region disposed in the first active region, an isolation structure disposed in the chop region, and a gate structure extending at least across the isolation structure in the chop region. The gate structure includes a gate electrode layer and a gate lining layer lining on the gate electrode layer. The gate lining layer includes a first portion having an upper surface that is lower than a bottom surface of the source/drain region.