Compliant parts have different characteristics from rigid parts and are used frequently in industries. One of the biggest challenges facing by industries is geometric variation management of these compliant parts which can directly impact product quality and functionality. Existing rigid body-based variation modeling approaches are not suitable for compliant assembly while finite element analysis-based methods have the disadvantages of requiring heavy computation efforts and detailed design information which is unavailable during preliminary design phase. Hence, this paper proposes a novel geometric variation propagation model of multi-station compliant assembly based on parametric space envelope. Three sources of variation: location-led positional variation, assembly deformation-induced variation, and station transition caused variation are analyzed. In this study, geometric variations are modeled indirectly through control points of constructed variation tool. Compared with existing methods where geometric variation is modeled by tracking key feature points on the manufacturing part, the proposed approach brings unique benefits. It can deal with arbitrary complex compliant part, and it provides a unified modeling framework for different types of variation. The method is illustrated and verified through a two-station three parts case study on a multi-station compliant panel assembly. The proposed method provides industries with a new way to manage geometric variation from compliant assembly.