The invention relates to an animal smell learning and training method and the system thereof, and the invention comprises the following steps: (1) before training animals, cut water supply for a long period of time, make animals have strong desire for finding water during training; (2) put animals into training ground, when training, supply the computer control system with two kinds of gas having various odors, then discharge them randomly in turn; (3) if under one kind of odor the animal licks water, it will be given some water as reward; while if under the other kind of odor the animal licks water, it will be given electric shocks as punishment; (4) test more than one hundred of times circularly like that, if animal can distinguish these two various odors, a correct operant conditioned reflex is created, according to the animal behaviour, whether the animal has the ability of distinguishing these two kinds of odors can be determined. The invention use multi-functional PCI data acquisition card, video capture card and control software in the system, so that it is able to control and record the experiment process automatically and analyze behaviors.