Objective To establish a model for different degrees of fear stress and explore the effect of fear stress on visual cognitive ability in Long-Evans rats. Methods Foot shock was used as a stress stimulus and a cognitive choice experiment was designed, and then the neural response of the amygdala was measured for functional network analysis to evaluate the effects of fear stress on visual cognition. First, the rats were divided into strong (S+) and weak (S) fear stress groups and a control group (N) and treated with different degrees of foot shock stimulation. Then, intensive visual cognitive training was conducted with a single image (“△”). Finally, a cognitive choice experiment was conducted with two images (“△”and “十”). We combined our results with the complex network theory to construct a visual cognitive functional network of the amygdala in rats under fear stress, in which the information transfer efficiency was represented by the average path length and clustering coefficient. Results The time required to complete intensive visual cognitive training was significantly higher in the groups S+ than S and N, and was significantly higher in the groups S than N at the early stage of intensive training but showed no significant difference at the later stage. In the cognitive choice experiment, a visual cognitive connection was formed in the groups S and N, while no visual cognitive connection was formed in the group S+. In the brain functional network analysis, effective visual information transmission was observed in the groups S and N, while no visual information transmission was observed in the group S+. Conclusions Fear stress has negative effects on visual cognition, and the cognitive effects become significantly worse as the degree of fear increases.