A gearbox in concrete mixer truck was used as an example to study the effect of system deformation on the misalignment of gear mesh by applying the methods of FEA and tooth contact analysis. The variation of misalignment under different stiffness of system was compared. Gear misalignment was calculated on the basis of the system deformation analysis. The calculation result was used to determine the parameter of lead modification. Finally, it is proved that the method of determining lead modification parameter is reliable by the simulation analysis.