The invention discloses a finger vein deep feature extraction and matching method and system based on incomplete complement. The finger vein deep feature extraction and matching method is characterized by comprising: preprocessing a finger vein image to be registered to obtain a preprocessed finger vein image to be registered; performing deep feature extraction training on the preprocessed fingervein image to be registered by adopting a deep convolutional neural network to obtain deep features of the finger vein image to be registered; performing registration by adopting the deep features ofthe finger vein image to be registered and constructing a template library for processing to obtain a registered template library reserving the deep features; acquiring a finger vein image to be recognized, extracting features from the finger vein image to be recognized to obtain deep features of the finger vein image to be recognized; and matching the deep features of the finger vein image to berecognized with the registered template library reserving the deep features to obtain a matching recognition result. By extracting high distinguishing features of the finger vein image, the matching precision is improved.