Bulk residual stress of component originating from material preparation processing has an impact on large-scale assembly deformation and consequently affects dimensional and shape accuracy of assembly especially for those thick and asymmetric components. This article proposes a quantitative variation propagation modeling method, highlighting the subsequent impact of initial residual stress in raw material, and provides an effective pattern mapping method between bulk stress fluctuation and overall component or assembly deformation. The basic analysis approach considering residual stress is validated by test experiments previously. Legendre polynomials and Spline functions are employed to represent stress perturbation pattern and localized deformation pattern, respectively. Variation propagation is modeled in a case study of the horizontal stabilizer assembly system based on these non-linear mathematical representations. The orthogonal test is designed utilizing finite element analysis to simulate principal stress component perturbation. Corresponding regression analysis aimed at the optimized geometric target is conducted leading to confined Legendre coefficients range for better match. The mapping relation is developed graphically between Legendre coefficient’s pattern and Spline coefficient’s pattern revealing the region of influence and offers assembly deformation prediction as well as practical component selection suggestion for better match. The downstream quality control can be further traced back to the parameter setting of material preparation processing like stretch ratio. The methods we present help systematically improving compliant assembly precision in consideration with residual stress factor in aircraft assembly structure.