For the application of low noise and high linearity in microwave photonic link, the influence of waveguide cross coupling effect of M-Z electro-optic modulator on harmonic suppression ratio was studied. Firstly, through the joint simulation of OptiBPM and MATLAB, it was found that the cross coupling effect between waveguides led to a shift of the modulator RF electrode and bias electrode operating point, and then reduced the harmonic suppression ratio. Secondly, the phenomenon was verified by a special lithium niobate modulator. At last, a method to detect the cross coupling effect of M-Z electro-optic modulator was proposed. This discovery not only breaks the blind area of the influence of waveguide structure on harmonic suppression ratio, but also provides a certain reference for the development of ridge waveguide and photonic crystal thin film lithium niobate modulator for microwave photonic technology.