The invention discloses a ship feature re-identification method, application method and system based on deep learning, and According to the method, a deep feature extraction network with the efficientprocessing capability in the field of image perception is used to extract the deep features with the distinction degree, the deep features with the high-level perception semantics is autonomously extracted, the change of pixel levels is not depended on, and the overall features are considered, so that the problems of overwater supervision, low ship information query efficiency and the like causedby inaccurate matching and high detection error rate are solved, and the target ship discrimination can be effectively carried out. The PCB partitioning and the matrix type operation matching have the good recognition effect for the ships only parts of which occur, the matching speed is high, the problems of ship transformation, hidden identity escape supervision and the like are solved, and theintelligent auxiliary effects on the maritime traffic management, accident investigation, water conservancy attack illegal sand mining, navigation channel ship gate passing charging, customs attack private activities and the like are achieved. Compared with a ship identification method in the prior art, the ship re-identification method has obvious advantages in efficiency, cost and accuracy.