The spatial filter in the beam shaping system of a 2 kW radio frequency slab CO2 laser is used to eliminate side lobes and improve quality of output beams. It is important to study the effect of misaligned spatial filters on the characteristics of the shaped beam. The effect of the misaligned spatial filter on intensity distribution of the shaped beam was studied theoretically and experimentally. The theoretical simulation results are in agreement with the experimental results. Meanwhile, the effect of the misaligned spatial filter on output power of the shaped beam was studied by theoretical simulation. The results show that the effect of lateral displacement in the unstable direction of the spatial filter on the output power and the intensity distribution of the shaped beam is significant. The output power decreases and the side lobes appear as the lateral displacement increases. The shaped beam is not a circle while the spatial filter is axially-misaligned. The diameter difference is up to 3 mm when the axial displacement is 10 mm. The angle misalignment of the spatial filter mainly has impact on the shaped beam in the waveguide direction. The side lobes appear and the beam quality decreases as the angle misalignment increases. The loss of output power is up to 25% when the angle misalignment is 10°.