Misalignment among stacked layers of absorbers is inevitable in practice. Adverse effects induced by this undesired factor was investigated and analyzed in this paper. The absorption responses of thin terahertz metamaterial (MM) absorber with different degree of misalignment were simulated by finite-difference time-domain (FDTD) method under both transverse magnetic (TM) and transverse electric (TE) polarization. Results show that slight misalignment deteriorates absorption response due to the decreased spatial resolution. The analyses are given in terms of the magnetic field distribution in the cross section. In addition, the depravation is changed with polarization, which depends on the direction of excursion.