A metamaterial absorber is designed and applied to the waveguide slot antenna. The absorber is composed of two metallic layers separated by a lossy dielectric spacer. The top layer consists of etched oblique cross-gap patch set in a periodic pattern and the bottom one is of a solid metal. By fine adjusting the geometric parameters of the structure, we can obtain a polarization-insensitive, wide-incident-angle ultra-thin absorber that has an absoption of 99.1% and a thickness of only 0.01λ. The absorber is applied to the waveguide slot antenna. The radar cross secction (RCS) of antenna is reduced by 3 dB or more in an the operation band from 5.48 GHz to 5.7 GHz, and by 5 dB or more in the boresight direction from -25° to +25°, and the most reduction value exceeds 12 dB, but the forward gain of antenna reduces only 0.53 dB. The experimental results are in good agreement with the simulation results, which verifies that the absorer has a good characteristic of RCS reduction and can be applied to the stealth of antenna.