Polyhedral oligomeric silsesquioxane (POSS) is a promising nanofiller for tuning properties of optically transparent polymer materials. On the other hand, traditional completely condensed POSS (CC-POSS) has a fundamental problem for fabricating optically transparent composite films; CC-POSS has high crystallinity due to its symmetrical structure, resulting in aggregation in the polymer matrices. In this work, we have demonstrated that incompletely-condensed POSS (IC-POSS), which has an open-cage structure, can be well dispersed in a poly(methyl methacrylate) (PMMA) matrix. IC-POSS with various substituents were readily synthesized, and their composite films of PMMA were fabricated by solution-casting method. High transparency was achieved with up to 30 wt % of the IC-POSS fillers, while the CC-POSS analogues caused phase separation with 10 wt % loading. Addition of the IC-POSS fillers can improve thermal stability and control glass transition temperature by the substituent structure. Additionally, refractive index was tuned from 1.485 to 1.513.