Shell structures refer to structural elements that derive strength and load-bearing capacity from their thin and curved geometry. In practical applications, shell structures are commonly composed of multiple patches to represent intricate and diverse architectural configurations faithfully. Nevertheless, the design of multi-patch shell structures holds considerable promise. However, most of the previous work is devoted to the numerical analysis of multi-patch shell structures without further optimization design. The work proposes an inverse design framework, specifically focusing on multi-patch configurations based on Reissner–Mindlin theory. First, reparameterization and global refinement operations are employed on the provided multi-patch shell structures. Renumbering the indices of control points with shared degrees of freedom at the interface naturally ensures C0-continuity between patches. Subsequently, this study investigates the amalgamation of Isogeometric Analysis (IGA) and the Solid Isotropic Material with Penalization (SIMP) method for topology optimization of shell structures. The proposed approach is validated through numerical examples, emphasizing its capacity to enhance multi-patch shell structure design, showcasing robustness and efficiency.