Dynamic crushing responses of honeycomb structures having irregular cell shapes and non-uniform cell wall thickness are studied using the Voronoi tessellation technique and the finite element (FE) method. FE models are constructed for such honeycomb structures based on Voronoi diagrams with different degrees of cell shape irregularity and cell wall thickness non-uniformity. The plateau stress, the densification strain energy and the initiation strain are determined using the FE models. Simulation results reveal that the “X” and “V” shaped deformation modes evident in a perfectly ordered honeycomb at low or moderate impact velocities are disrupted as cell shapes become irregular and/or cell wall thickness gets non-uniform. The “I” shaped deformation mode is clearly seen in all honeycomb structures at high impact velocities. Both the plateau stress and the densification strain energy are found to decrease as the degree of cell shape irregularity or the degree of cell wall thickness non-uniformity increases, with the weakening effect induced by the presence of non-uniform cell wall thickness being more significant. When the two types of imperfections co-exist in a honeycomb structure, the interaction between them is seen to exhibit a complicated pattern and to have a nonlinear effect on both the plateau stress and the densification strain energy. It is also found that stress waves propagate faster in a honeycomb structure having irregular cell shapes and slower in a honeycomb structure having non-uniform cell wall thickness than in a perfectly ordered honeycomb. Finally, the strain hardening of the cell wall material is seen to have a strengthening effect on the plateau stress, which is more significant for perfectly ordered honeycombs than for imperfect honeycomb structures.