A novel method to design an ultra-thin perfect metamaterial absorber (PMA) with high quality factor (Q-factor) at microwave frequencies is proposed to improve the absorption performance. The PMA achieves a high Q-factor by appropriately loading the metal cavity based on the substrate integrated waveguide (SIW) technology and the common PMA. An ultrathin absorber with a thickness of 0.0065λ and a full-width at half-maximum of 5.8% is designed. The Q-factor of absorptivity of the absorber is 33.9, which is enhanced by 20% compared with that of the conventional PMA. Meanwhile its Q-factors for radar cross section (RCS) reductions of 1.5 and 3 dBsm respectively increase 54% and 67% higher than those of the conventional PMA. The measured results show that the proposed SIW-PMA eliminates the frequency drift between the infinite periodic array and the finite periodic array, which occurs in the conventional design process. The simulated and measured results show that the proposed PMA has high Q-factor of absorptivity and excellent effect of RCS reduction. Its RCS reduction can reach a maximum value of 14.1 dBsm at the response frequency.