The unstable-waveguide hybrid resonator emits a rectangular, simple astigmatic beam with a large number of high-spatial-frequency oscillations in the unstable direction. To equalize the beam quality, in this paper, a beam shaping system with a spatial filter for the hybrid resonator was investigated by numerical simulation and experimental method. The high-frequency components and fundamental mode of the output beam of the hybrid resonator in the unstable direction are separated by a focus lens. The high-frequency components of the beam are eliminated by the following spatial filter. A nearly Gaussian-shaped beam with approximately equal beam propagation factor M² in the two orthogonal directions was obtained. The effects of the width of the spatial filter on the beam quality, power loss, and intensity distribution of the shaped beam were investigated. The M² factor in the unstable direction is changed from 1.6 to 1.1 by optimum design. The power loss is only 9.5%. The simulation results are in good agreement with the experimental results.