Hypernetwork is a useful way to depict multiple connections between nodes, making it an ideal tool for representing complex relationships in network science. In recent years, there has been a marked increase in studies on hypernetworks, however, the comparison of the difference between two hypernetworks has been given less attention. This paper proposes a hyper-distance-based method (HD) for comparing hypernetworks. This method takes into account high-order information, such as the high-order distance between nodes. The experiments carried out on synthetic hypernetworks have shown that HD is capable of distinguishing between hypernetworks generated with different parameters, and it is successful in the classification of hypernetworks. Furthermore, HD outperforms current state-of-the-art baselines to distinguish empirical hypernetworks when hyperedges are disrupted.