With the advent of Computer-Aided Design, the design and fabrication of complex free-form shells have become easier to achieve. However, this results in extensive usage of custom-made formworks for the production of shell components and falseworks which provide support for the shell during the construction process. Therefore, a modular design method is proposed for generating form-active spatial structures out of stackable blocks of a few types, having in mind its potential applications such as housing. Instead of shells, spatial masonry structures are thus the main consideration in the design process considering building on top of a vaulted ceiling. By designing a 3D interlocking grid and introducing a four-step topological design that is coupled with structural verification processes based on finite element modelling and discrete element modelling simulations, the geometry of interlocking stackable modular blocks can be automatically generated for constructing such spatial masonry structures. The proposed method ensures that the designed vaults are modular, reconfigurable, and self-supporting during construction, thus increasing the efficiency of mass production while allowing for combinatorial mass customization in designs.