A terahertz (THz) metamaterial design mechanism based on a stacked chip is proposed. Unlike the traditional sandwich-type metamaterial design mechanism based on the “resonant layer–dielectric layer–ground layer” structure, it adopts a stacked design of upper and lower metamaterial chips to achieve a new structure based on the “dielectric layer–resonant layer–air layer–ground layer” structure. This could break through the thickness limitations and construct an ultra-thin metamaterial upper chip. To verify the effectiveness of this method, we applied it to the field of THz perfect absorbers. We designed, simulated, and prepared a terahertz stacked chip-based perfect absorber with an upper-chip thickness less than 1/800 of the wavelength. Then, a reflective spectroscopy system based on a vector network analyzer is built to test the absorption performance. The measured results show that it has an absorptivity of 98.4% at 0.222 THz, which is in good agreement with simulations.