In this paper, we propose a pairwise key distribution scheme based on a novel interconnection graph termed Hierarchical Hypercube. Motivated by the fact that sensor nodes are often deployed in groups (for example, dropped from an airplane at different locations) and hence the whole network is composed of multiple such groups, we design Hierarchical Hypercube as a two layer topology, where each group is modeled by an inner hypercube and connections between the groups are modeled using an outer hypercube. we propose a topology termed Hierarchy Hypercube. While retaining the desirable properties already shown by existing pairwise schemes, by using Hierarchical Hypercube, direct communication from a node to any other nodes is not required, either within a group or among groups, and hence this topology can effectively and realistically reflect the connectivity of the physical sensor network deployed in groups. Furthermore, we propose key pre-distribution scheme based on this novel topology and show that the new scheme possesses high probability of direct key establishment, low memory overhead, and resilience in the presence of broken communication links and compromised nodes, and thus still retain the desirable properties even when the ideal logical connection are distorted in the real deployment.