The invention discloses an intelligent vein authentication method and system having autonomous learning capability. The method comprises steps that model training of the full convolutional neural network depth learning model in repeated and regular global training and irregular local training modes is carried out, before online operation of the full convolutional neural network depth learning model, one global training is carried out through utilizing accumulated samples, and optimized characteristic extraction, characteristic identification and characteristic classification parameters are stored; after online operation of the model, newly-registered samples are utilized to carry out irregular local training of the model, and characteristic classification parameter optimization is completed; under the specific condition, the newly-accumulated samples are utilized to carry out regular global training of the model, and the characteristic extraction, characteristic identification and characteristic classification parameters are optimized for another time, the model is guaranteed to be the intelligent authentication system having the autonomous learning capability, and vein authentication precision is further enhanced.