A secure synchronization apparatus, method, and non-transitory computer readable storage medium thereof are provided. The secure synchronization apparatus of the present invention includes a storage unit, an interface, and a processing unit. The interface is electrically connected to a storage server via a network. The processing unit is electrically connected to the storage unit and the interface. The processing unit is configured to execute an operating system and execute an agent program installed on the operating system. The agent program configures an isolated space, manages an extended space within the storage unit, and synchronizes an object between the isolated space, extended space, and the storage server through the interface. The isolated space and the extended space are only recognized by the agent program installed on the operating system and the object in the two spaces is accessible only via the agent program.