A shared directory management system includes a storage module, a first cluster server, a second cluster server, and a management module. In the normal mode, the first cluster server controls the storage module, the management module examines the storage module using a monitor method, and if the storage module was processed by an update action, the management module stores update setting information corresponding to the update action into a database. If failure occurs, the second clustered server controls the storage module, the management module returns the storage module according to the update setting information stored in the database, and switches back to the normal mode.