Mesoporous nanomaterials have attracted widespread interest because of their structural versatility for applications including catalysis, separation, and nanomedicine. We report a one-pot synthesis method for a class of mesoporous silica nanoparticles (MSNs) containing both cubic and hexagonally structured compartments within one particle. These multicompartment MSNs (mc-MSNs) consist of a core with cage-like cubic mesoporous morphology and up to four branches with hexagonally packed cylindrical mesopores epitaxially growing out of the cubic core vertices. The extent of cylindrical mesostructure growth can be controlled via a single additive in the synthesis. Results suggest a path toward high levels of architectural complexity in locally amorphous, mesostructured nanoparticles, which could enable tuning of different pore environments of the same particle for specific chemistries in catalysis or drug delivery.