An apparatus and method for reorganizing mapping information in a flash memory are provided. The apparatus includes a sector-managing module that secures a mapping sector where mapping information is recorded in a physical unit, and determines whether user data is recorded up to a sector located in a predetermined position, and a mapping-information-recording module that records the mapping information in the mapping sector according to a result of the determination. Here, the mapping information includes a relation of a physical sector storing the user data and a logical sector corresponding to the physical sector.