The influences of two classical defects on the compressive mechanical properties of honeycombs are investigated in this paper. The numerical results show that the bigger concentrated hole has more significant effects on the mechanical behavior of honeycombs than the smaller scattered holes. The bigger concentrated hole even can change the deformation mechanism of honeycombs. Furthermore, we find that a honeycomb with some filled cells has a higher Young's modulus. At the same time, the buckling stress of a filled elastic honeycomb can be enhanced. But, the plastic collapse stress of a filled elastic-plastic honeycomb may keep unchanged or drop a little.