[Objective] With advancements in three-dimensional integration technology, wafer stacking has become a critical process for enhancing semiconductor device performance in the post-Moore era. The reliability of interfacial electrical interconnections depends on the bonding overlay accuracy, which is now primarily limited by residuals at the 50 nm level. This study addresses the challenge of bonding residuals in high-precision wafer bonding, which arise from the coupled effects of wafer elastic deformation, clamping constraints, and bond wave propagation. Existing models often lack comprehensive multiphysics coupling or fail to establish a link between specific process parameters and residual formation, limiting their use in process optimization. Therefore, developing a high-fidelity coupled model is essential for understanding the residual generation mechanism and devising effective suppression strategies. [Methods] A multiphysics coupling analysis model was developed that comprehensively considers wafer anisotropy, clamping boundary effects, and bond wave propagation behavior. The framework integrates anisotropic thin-plate elasticity (incorporating crystal orientation transformation tensors), gas film dynamics (governed by a modified Reynolds equation with bonding stress), and contact mechanics (solved via the augmented Lagrangian method). Bond wave propagation is governed by an energy criterion at the wavefront, balancing effective bonding energy against strain energy and the work performed by gas film and mechanical contact pressures. A finite element model for the 300 mm wafer bonding process was developed, achieving submicron accuracy. Key numerical strategies included a staggered iterative scheme for updating the wavefront, bonding force, gas pressure, and structural deformation; adaptive time stepping based on residual variations; and stabilization damping to suppress rigid body motion. Model validity was confirmed through comparison between simulation predictions and experimental pattern wafer geometry measurements. [Results] The simulation accurately captured the nonuniform bond wave propagation induced by wafer anisotropy. The stress and residual distributions exhibited a distinct fourfold symmetry consistent with the crystallographic orientation. Residuals were primarily concentrated near the wafer edge, with additional significant residuals observed at the center-consistent with previous reports. Experimental validation showed strong agreement between simulated and measured residual distribution patterns. Systematic parameter studies revealed that using a flat bond head reduced the 2-norm of the residual vector by 41% compared with a spherical head (0.63 μm vs. 1.07 μm). Employing a lower-stiffness material (polyethylene) for the bond head reduced the residual 2-norm by 23% compared with PEEK plastic. Moreover, an increase in the initial wafer gap correlated with a higher residual 3σ value. [Conclusions] This study establishes a robust multiphysics coupling and process co-optimization framework for high-precision wafer bonding. The proposed model effectively captures the combined effects of wafer anisotropy, gas film dynamics, and contact mechanics on residual formation, enabling high-fidelity simulation of the bonding process and quantitative analysis of key process parameters. The findings demonstrate that optimizing the bond head design-with a flat surface and low-stiffness material-and minimizing the initial wafer gap can significantly suppress bonding residuals. This work provides a theoretical basis and practical design guidelines for optimizing wafer bonding processes to achieve superior overlay accuracy.