With advances in 3D printing technology, now honeycomb structures can be made with virtually unlimited unit cell geometries and cell arrangements giving a wide range of possible mechanical properties. However, studies on such structures have been mainly limited to the hexagonal honeycombs with little work done on other cell geometries. This paper investigates the effect of unit cell geometry on the in-plane compressive response and energy absorption behaviour of honeycombs using full-scale non-linear numerical simulations. Nine types of honeycombs are designed from different unit cell shapes, but having the same relative density. Finite element analysis is used to simulate the honeycombs’ behaviour under uniaxial compression loading. The results showed that unit cell geometry and cell arrangement affect the honeycombs’ compressive response significantly and provide different energy absorption characteristics. This comparison study shows that the honeycombs in which the deformation mode is dominated by bending of cell edges present a lower stiffness (effective modulus) and compressive strength, but a smoother plateau stress. The honeycombs having their deformation mode dominated by plastic buckling present a higher stiffness with less stable and undulated plateau stress. The results of this study provide more understanding in predicting the global behaviour of honeycomb structures and their energy absorption characteristic through their micro-topology. The effect of cell shape and its arrangement on the selection of honeycombs for energy absorption application is discussed and a methodology is proposed to balance the energy absorption with maximum transmitted stress, which is crucial for energy-absorbing design of structures.