The present invention provides a paper document recovery system and recovery method. The recovery system comprises an identity authentication unit, a display and control panel, an upper cover, a sliding rail, a scanning head, housing, a paper transport, a paper separation mechanism, a transition region, a storage box and a central control unit. The paper separation mechanism includes a slideway, paper-pressing glass, a first motor, a paper separation rotary table, a paper separation stripe, a paper separation baffle, an upper paper deflector, a lower paper deflector, an upper runner, a lower runner and a second motor. The transition region includes a transition region door, a pressing board, a third motor, a first lead screw, a fourth motor, a second lead screw, a feed belt, a fifth motor, a sliding block, a polished lever and a pallet. The storage box includes a first storage warehouse, a second storage warehouse, an infrared ray sensor, a roller, an electric control lock and a frame of the storage box. The present invention discloses a document recovery method based on the paper document recovery system at the same time so as to realize the self-service recovery of documents with unattended operation, with fast recovery speed and high accuracy.