The optical elements’ maladjustment is a potential threaten in optical systems, thus, the transmission feature of laser beams passing through a misaligned optical system is widely studied. By using approximate expansion of circle diaphragm and generalized Huygens-Fresnel diffraction formula, a universal analytic expression is deduced for the flat-topped multi-Gaussian beams passing through a misaligned optical system with two-lens and two-diaphragm. The study on the propagating property of fundamental-mode Gaussian beams and a flat-topped multi-Gaussian beam is carried out accordingly. The expansion of complex Gauss function of misaligned optical circle diaphragm is given, as well as a group of new parameter values of the expansion of complex Gauss function. By using the new parameter values, the influence of disadjust parameters on output intensity distribution is analyzed numerically. The result shows that the diaphragms’ offset can make the beams offset or covered, and the second diaphragm influences more; the angle deflection of diaphragms can make light beams compressed in the deflection direction, and the first diaphragm influences more; the offset of the first lens can weaken light intensity in the same direction of the lens offset, and the offset of the second lens can weaken light intensity in the opposite direction of the lens offset; the angle deflection of the first lens can make light beams move to the opposite direction, and the angle deflection of the second lens has no influence; when all the diaphragms and the lenses are disadjust, the angle deflection of the first lens has a vital influence to the output intensity distribution.