Provided are a three-dimensional (3D) memory device and a manufacturing method thereof. The 3D memory device includes a gate stacked structure, a channel layer, a charge storage structure, an electrode layer and a capacitor dielectric layer. The gate stacked structure is disposed on a substrate and includes a plurality of gate layers electrically insulated from each other. The gate stacked structure has at least one channel hole and at least one capacitor trench. The channel layer is disposed on the sidewall of the at least one channel hole. The charge storage structure is disposed between the channel layer and the sidewall of the at least one channel hole. The electrode layer is disposed on the sidewall of the at least one capacitor trench. The capacitor dielectric layer is disposed between the electrode layer and the sidewall of the at least one capacitor trench.