Large-scale composite structures are widely used in aerospace due to their high strength-to-weight ratio, lightweight properties, and corrosion resistance. Key applications include large phased-array antenna panels, composite wing boxes, and rocket fairings. For instance, composite honeycomb sandwich antenna panels are critical for satellite functionality but face structural deformations in harsh space environments, threatening performance and safety. Thus, deformation monitoring for these components is urgently needed. The inverse Finite Element Method (iFEM) is a promising deformation monitoring technique, as it requires no structural parameters or prior data and enables 3D deformation analysis. iFEM discretizes structures into elements, calculates theoretical strains via nodal displacements, and minimizes errors between theoretical and measured strains to determine deformations. However, traditional iFEM struggles to balance high precision and real-time processing under complex aerospace loading and boundary conditions, limiting practical use. To address this, this study optimizes the error function of iFEM, further improve the refactoring accuracy for composite antenna panels. Simulations and experiments confirm that the improved method achieves higher deformation monitoring precision while maintaining computational efficiency. This advancement offers reliable support for structural health monitoring in complex operational scenarios, strengthening the applicability of iFEM in mission-critical aerospace systems.