A generic and effective approach for solving the aggregation effect observed with optical materials in solid state or in a solution with a poor solvent was explored by designing two types of squaraine-containing polyhedral oligomeric silsesquoixane (POSS)-based hybrids. It is expected that incorporation of “huge” inorganic POSS nanoparticles into optical materials via covalent bonding can effectively decrease the strong dipole–dipole and π–π stacking interactions, inhibit intermolecular charge transfer between adjacent squaraine molecules, and improve optical, thermal and chemical stability of the resultant materials. Both theoretical calculations and experimental results indicate that the molecular design strategy is rational and efficacious. The resultant organic–inorganic hybrid optical materials effectively eliminate the aggregation of organic optical chromophoric groups by hindering intermolecular charge transfer and decreasing dipole–dipole and π–π stacking interaction between the chromophores, and exhibit good optical stability, i.e., the absorption peaks of H1 and H2 display only a slight blue-shift, even in the solid. Simultaneously, the hybrids also show significantly enhanced thermal, and chemical stabilities in comparison with the precursor organic optical materials.