A deduplication memory system includes a virtual memory space, a physical memory space and a memory manager. The memory manager generates a user data entry that is stored in the physical memory space. The user data entry represents a unique user data of a predetermined granularity appearing in the virtual memory space, and includes first and second portions. The first portion includes information relating to a number of duplication times the unique user data corresponding to the user data entry is duplicated in the virtual memory space, and the second portion includes a selected part of the unique user data from which the unique user data may be reconstructed. The first portion may include an index to an extended reference counter table or a special data pattern table if the number of duplication times of the unique user data is greater than or equal to a predetermined number.