Large flexible aircraft are often accompanied by large deformations during flight leading to obvious geometric nonlinearities in response. Geometric nonlinear dynamic response simulations based on full-order models often carry unbearable computing burden. Meanwhile, geometric nonlinearities are caused by large flexible wings in most cases and the deformation of fuselages is small. Analyzing the whole aircraft as a nonlinear structure will greatly increase the analysis complexity and cost. The analysis of complicated aircraft structures can be more efficient and simplified if subcomponents can be divided and treated. This paper aims to develop a hybrid interface substructure synthesis method by expanding the nonlinear reduced-order model (ROM) with the implicit condensation and expansion (ICE) approach, to estimate the dynamic transient response for aircraft structures including geometric nonlinearities. A small number of linear modes are used to construct a nonlinear ROM for substructures with large deformation, and linear substructures with small deformation can also be assembled comprehensively. The method proposed is compatible with finite element method (FEM), allowing for realistic engineering model analysis. Numerical examples with large flexible aircraft models are calculated to validate the accuracy and efficiency of this method contrasted with nonlinear FEM.