The invention provides a memory device and a manufacturing method thereof. The memory device includes a substrate, a capacitor, a protection device, a first metal interconnect, and a second metal interconnect. The capacitor is located on the substrate of a first region. The protection device is located in the substrate of a second region. The capacitor includes a plurality of bottom electrodes, a top electrode, and a capacitor dielectric layer. The top electrode has a first portion and a second portion, wherein the second portion is extended to the second region. The capacitor dielectric layer is located between the bottom electrodes and the top electrode. The first metal interconnect is located between the capacitor and the substrate. The second metal interconnect is located between the second portion of the top electrode and the protection device. The top electrode is electrically connected to the protection device through the second metal interconnect.