Epoxy/zirconia hybrid materials were synthesized via in situ polymerization of acetic acid-modified zirconium alkoxide. The reactivity of acetic acid-modified zirconium alkoxide changed with the amount of acetic acid added. In the hybrid materials, the phase structure varied between the homogeneous phase and nanophase separation as the reactivity of zirconium alkoxide changed. At the molecular level, the storage modulus in the rubbery region significantly increased and the peak area of tan delta in the glass-transition temperature region decreased with increasing zirconia contents in the hybrid dispersed zirconia. Additionally, the optical properties of the hybrid materials in the homogeneous phase were better than those in the system with nanophase separation.