An integrated circuit device includes a substrate, a first isolation feature, a memory cell, and a semiconductor device. The substrate has a cell region, a peripheral region, and a transition region between the cell region and the peripheral region. The first isolation feature is in the transition region. The substrate includes a protrusion portion between a first portion and a second portion of the first isolation feature, the second portion is between the first portion and the cell region, and a top surface of the first portion of the first isolation feature has a first part and a second part lower than the first part, and the second part is between the first part and the second portion of the first isolation feature. The memory cell is over the cell region of the substrate. The semiconductor device is over the peripheral region of the substrate.