Composite structures are widely used due to their superior properties, such as low density, high strength, and high stiffness-to-weight ratio (Mallick, 1993, Fiber-Reinforced Composites: Materials, Manufacturing, and Design, Marcel Dekker, New York). However, the lack of methodologies for variation modeling and analysis of composite part assembly has imposed a significant constraint on developing dimensional control for composite assembly processes. This paper develops a modeling method to predict assembly deviation for compliant composite parts in a single-station assembly process. The approach is discussed in two steps: considering the part manufacturing error (PME) only and considering both the PME and the fixture position error (FPE). Finite element method (FEM) and homogenous coordinate transformation are used to reveal the impact of the PME and the FPE. The validity of the method is verified with two case studies on assembly deviation prediction of two composite laminated plates considering the PME only and both the PME and the FPE, respectively. The proposed method provides the basis for assembly deviation prediction in the multistation composite assembly.