The assembly precision of wheel alignment parameters is vital to vehicle handling stability. Due to the vertical wheel displacement and compliant components in suspension systems, it is difficult to assemble qualified vehicles with proper wheel alignment parameters. In the assembly shop of the automobile factory, the adjustment of wheel alignment parameters is the most time-consuming process because it relies on trial and error. In order to provide a theoretical guidance to the precision control of wheel alignment parameters, this paper extends the theory of equilibrium equations of incremental forces (EEIF) to 3D compliant mechanisms. Constraint equations of kinematic joints are adopted to express the spatial relationships of different parts. A couple of fixed and floating joint coordinate systems (CSs) are used together to represent deviations of compliant components. The impacts of suspension part deviations on vertical wheel displacement and assembly deformations are well illustrated by such approach. Accuracy of the proposed method is verified by comparing with ADAMS simulation. The results show that the error rates of the 3D EEIF method are less than 5%. Furthermore, statistical assembly variation analysis of a Macpherson suspension is accomplished by using the proposed method and an optimized process strategy is put forward.