A method of reducing the in-band radar cross section (RCS) of waveguide slot array antenna by utilizing a metamaterial absorber (MA) is preflented. A novel ultra-thin (the thickness is only 0.01λ, λ is the wavelength corresponding to the MA resonant frequency) MA with high absorptivity and no surface lossy layer is designed; the absorber is composed of two metallic layers separated by a lossy dielectric spacer. The top layer consists of an etched oblique cross-gap patch set in a periodic pattern and the bottom one is a solid metal. Effective impedance of MMA will match the free space impedance by adjusting the dimensions of electric resonant component and magnetic resonant component in the unit cell, and so the reflection will be minimized. Meanwhile, the MMA can obtain a resonant loss to fulfill the high absorption. By finely adjusting the geometric parameters of the structure, we obtain the MA with absorption 99.9%, and its absorbing mechanism being interprefled by analyzing surface current, surface electric field, and volume power loss density distribution, respectively. The metallic area between slots in E plane direction of waveguide slot array antenna is covered by MA, and a distance between the radiating slot and the MA is suitably arranged. Antenna radiation performance is kept in good order because this arrangement does not destroy the amplitude distribution of antenna aperture, and the high absorptivity of MA that contributes the reduction of structure mode scattering. Simulation and experimental results demonstrate that the array antenna loaded with MA gets more than 6 dB RCS reduction both in the x-and y-polarized incident conditions; and the RCS of antenna has obviously a reduction from -25° to +25°, the most reduction value exceeds 10 dB in the boresight direction, while the reflectance, gain and beam width are guaranteed. This idea has an important significance and engineering application for the RCS reduction of array antenna.