A storage device and a refresh method thereof are provided. The storage device includes at least a first processing core configured to operate by receiving a first power from a host, a second processing core separate from the first processing core, at least a first three-dimensional (3D) flash memory, a power module and a retention management module supplied with a second power from the power module when the first power is not supplied from the host. The retention management module is configured to refresh a part of the first 3D flash memory using the second processing core. The retention management module is configured to be woken up at intervals of a first period to refresh the part of the first 3D flash memory.