Unconventional aircraft configurations are of substantial interest in aircraft design re- search. A challenge is that the design of unconventional aircraft is often a multidisciplinary and high-dimensional problem. Therefore, traditional empirical models are often inadequate. Large-scale multidisciplinary design, analysis, and optimization (MDAO) has evolved as a potential solution to this problem. In this thesis, I present a novel mesh generation method that is compatible with a large-scale MDAO framework, which means the generated structural meshes can be easily updated in response to changes in shape design variables. The mesh generation algorithm starts with a B-spline based geometry that defines the aircraft’s structural components, such as the outer skin and the internal members. Initial triangular meshes are generated under the constraint of the intersection connectivity between different components. Next, all the meshes of the components are subjected to a series of mesh quality improvement procedures that involve splitting, merging, and smoothing optimizations. Lastly, the resulting quad-dominant meshes are transformed into fully quadrilateral meshes. I also validate the quality of the generated meshes and their finite-element shell analysis results. The results show that this algorithm is versatile, efficient, effective, and compatible with large-scale MDAO processes.