Ship assembly involves thousands of large dimensional compliant metal plates. These compliant metal plates are fully welded together by seam welding in the assembly process. Different from the automobile and aerospace assembly process, the final variation of ship assembly is significantly influenced by the geometric nonlinearity and welding deformation generated during the seam welding process. This paper develops a nonlinear variation model (NVM) to consider the geometric nonlinearity, welding shrinkage, and angular distortion based on elastic mechanics. Furthermore, the nonlinear variation model is calibrated by the composite Gaussian process (CGP) to compensate for other factors that are not considered in the nonlinear variation model. The proposed model is validated by a case study on the deviation prediction of an assembly of two compliant metal plates and compared with the existing methods. The results show that the proposed model has a significant improvement in prediction accuracy of assembly deviation.