Here, highly transparent nanocomposite films with an adjustable refractive index were fabricated through stable dispersion of ZrO2 (n = 2.16) nanoparticles (NPs) subjected to surface modification with SiO2 (n = 1.46) in polydimethylsiloxane (PDMS) (n = 1.42) using the Stöber method. ZrO2 NPs (13.7 nm) were synthesized using conventional hydrothermal synthesis, and their surface modification with SiO2 (ZrO2@SiO2 NPs) was controlled by varying the reaction time (3–54 h). The surface modification of the NPs was characterized using Fourier-transform infrared spectroscopy, dynamic light scattering, X-ray photoelectron spectroscopy, scanning electron microscopy, transmission electron microscopy, and ellipsometry. The surface modification was monitored, and the effective layer thickness of SiO2 varied from 0.1 nm to 4.2 nm. The effective refractive index of the ZrO2@SiO2 NPs at λ = 633 nm was gradually reduced from 2.16 to 1.63. The 100 nm nanocomposite film was prepared by spin-coating the dispersion of ZrO2@SiO2 NPs in PDMS on the coverslip. The nanocomposite film prepared using ZrO2@SiO2 NPs with a reaction time of 18 h (ZrO2@SiO2-18h-PDMS) exhibited excellent optical transparency (Taverage = 91.1%), close to the transparency of the coverslip (Taverage = 91.4%) in the visible range, and an adjustable refractive index (n = 1.42–1.60) as the NP content in the film increased from 0 to 50.0 wt%.