Hierarchical assemblies of perylenetetracarboxylic diimide bridged silsesquioxane (PDBS) with controlled structure at multi-length scale are studied using both experimental and computational methods. The organization process spans multi-length scales and includes three continuous steps: 1) stacking of the preprogrammed molecules into small clusters, 2) growing of the small clusters into nanoscale building blocks with various sizes and shapes depending on the experimental conditions, and 3) aggregation of nanoscale building blocks into micro-or macro-scale assemblies. The main factors determining the assembly morphology are the second and third steps, which can be controlled by varying the experimental conditions, such as solution drying rate, solvent composition, and PDBS concentration. Despite the different morphologies, all of these assemblies possess highly ordered lamellar structure. It is found that incorporating perylenetetracarboxylic diimide (PD) moieties into the highly ordered silica network endows the PD components with high thermal and mechanical stability, as well as improved optical and electronic properties.