Purpose To investigate the topological structure differences between the migraine patients group and the normal control group by using resting-state brain complex networks constructed based on graph theory. Materials and Methods Resting-state functional magnetic resonance imaging dataset were obtained from 22 migraine patients and 22 normal subjects. The functional complex networks of the two groups were constructed, and parameters including average clustering coefficient, characteristic path length, small worldness, assortativity, and betweenness of the two groups were respectively calculated. Results When compared with the parameters of normal control group, average clustering coefficient of migraine patients group was larger, small worldness and assortativity were also changed. The characteristic path length of the caudate nucleus and putamen areas presented abnormal in the migraine patients group. Betweenness centrality of the thalamus, inferior occipital gyrus and occipital gyrus increased in the migraine patients group. Conclusion The abnormal brain regions in the migraine patients group were mainly associated with pain processing, visual processing and sensory information relay. This study may contribute to better understanding and interpreting corresponding clinical condition of migraine.