Hierarchical structured materials represent an interesting platform for many potential applications such as separation, catalyst and drug delivery etc. However, controlled fabrication of this special structure still remains a big challenge. In the present work, a controllable sol-gel procedure was developed to precisely fabricate polysilsesquioxane particles with bowls-on-sphere structure from mixed organoalkoxysilane precursors with sodium ligninsulfonate as surfactant and polystyrene spheres as structure-directing agents. The morphology of the particles can be fine-tuned by judiciously adjusting the ratio of two silane precursors, amount of ammonia, surfactant content and polystyrene amount. The formation mechanism of spheres-on-sphere structured polysilsesquioxane particles was explored.