A semiconductor device includes a semiconductor substrate having an active region comprising a gate area, a bit line contact area and a storage node contact area. A recess is formed in the gate area and the bit line contact area. A gate is formed over the gate area and a portion of an isolation layer adjacent to the gate area. The gate includes a main gate in the gate area and a passing gate over the isolation layer. A first junction area is formed in the storage node contact area of the active region. A second junction area is formed in the bit line contact area of the active region. A first landing plug and a second landing plug are formed over the first junction area and the second junction area, respectively.