This paper focuses on the configuration reconstruction method based on substructural modes to identify the current configuration of assembled system of flexible modules in the on-orbit assembly engineering. At present, measurement system for monitoring large-scale ground structures has been very mature, and real-time reconstruction of structural deformation using measured strain datas has served as a key technology for actuation and control of flexible structures. However, little attention has been paid to solve the assembled system of flexible modules with variable configuration at different assembly stages. As assembly progresses, the monitoring and reconstructing of flexible assembled structures must overcome the challenges arising from their large-scale property and variable configuration. To tackle these two critical characteristics, this paper proposes a method and strategy for configuration reconstruction of flexible assembled structures based on substructural modes. The normal modes and constraint modes of substructure are introduced to construct the augmented strain modes. These augmented strain modes describe the variable constraints between substructures at different assembly stages. The strain-to-displacement transformation based on discrete strain measurements is derived to sense the deformation of substructure. The reconstruction sequence is designed to transmit the connection relationships and pose information of each substructure. Subsequently, the constraint modes and float frame reference of each substructure are updated. Combining the float frame reference and deformation field, the spatial configuration parameters of the entire assembly structure are reconstructed. Finally, numerical cases are conducted on an assembled antenna panel structure and an assembled parabolic truss structure. The effectiveness and feasibility of the proposed configuration reconstruction method are validated by comparing the forward static loading results with the reconstructed results.