The increase of thickness for large thin-walled structure causes the nonlinear enhancement of local structural stiffness, which leads to that the variation is concentrated on the local assembled area. The strong geometrical nonlinearity exists in the assembly process, which causes the non-uniform constraint for the material in assembled area and the variation of assembled large thin-walled structure is difficultly predicted. In this paper, the large thin-walled structure is partitioned into the assembled area and non-assembled area. The nonlinear stiffness matrix of each area is constructed based on continuum mechanics theory. The large non-assembled area is condensed as the nonlinear stiffness constraint and attached on the small assembled area. The non-uniform stiffness condensation method is developed and a new assembly variation model is proposed for large thin-walled structure with high local stiffness. The initial bending and torsional variations are constructed according to the manufacturing process of thin-walled structure and the assembly variations of two large cylindrical thin-walled structures are calculated. The predicted results by using the non-uniform condensation model are compared with that by the commercial software and the classic method of influence coefficients, in which the accuracy of the proposed model is verified. The proposed model may predict the local variation characteristics of large thin-walled structures effectively and is significant for the analysis of variation propagation in the series assembly process of large thin-walled structures.