Composite wings with inherent morphological integration characteristics can demonstrate exceptional load-bearing and aerodynamic performance through thoughtful design, garnering significant interest from researchers in recent years. This paper addressed the optimization challenge related to the coupling of the main structural layout, dimensions, and layup sequence of composite wings. By taking into account design constraints such as strength, stiffness, mode, and manufacturing processes, we proposed a dual-layer optimization strategy for topology and size based on the concept of the ground structural method. Optimization and solution were achieved using duality theory, ultimately leading to a collaborative layout-size optimization design for composite materials. Furthermore, the methodology was validated using a UAV’s all-composite wing as a case study. The results confirmed the strong effectiveness and practicality of the collaborative optimization approach discussed in this paper.