Geometric deviations and clamping constraints are the two major variation factors in thin-walled structure assembly processes. Geometric deviations are caused by inevitable uncertainties in manufacturing processes and have a significant impact on dimensional control for compliant assembly processes. Due to the flexibility of thin-walled structures, the clamping constraints during assembly greatly affect the compliant deformation of assembled structures. In this paper, a new method based on isogeometric analysis (IGA) considering geometric deviations and clamping constraints is proposed. The geometric deviations of thin-walled structures can be obtained by offsetting along the control points in an ideal part based on Nonuniform Rational B-Splines (NURBS), and the clamping constraints, such as fixture positioning deviations and connection matching deviations, are converted into displacement boundary conditions by the Lagrange multiplier method. Furthermore, the elastic force induced by initial geometric deviations is calculated using Kirchhoff-Love shell elements. Considering the coordination constraint relationship between shape closure and force closure in the compliant assembly process, a variation propagation model is developed using NURBS-based IGA. It integrates geometric deviations and compliant deformations into a unified mathematical representation framework by embedding exact geometry into assembly analysis. In addition, a numerical example is presented to demonstrate the accuracy and effectiveness of the developed method.