The generalized analytical expression for the propagation of flat-topped multi-Gaussian beams through a misaligned apertured ABCD optical system is derived. Using this analytical expression, the propagation characteristics of flat-topped multi-Gaussian beams through a spatial filter are investigated. The analytical formula of the electric field distribution in the focal plane is also derived for revealing the effects of the misalignment parameters clearly. It is found that different misalignment parameters have different influences on the electric field distributions of the beam focus spot and the output beam characteristics. The intensity distribution of the beam is mainly determined by the misalignment matrix element E, and the phase distribution is affected by the misalignment matrix elements G and E.