Nc-SiOx/a-SiOx multilayer films were deposited using very-high-frequency plasma enhanced chemical vapor deposition (VHF-PECVD), to investigate the application of silicon quantum dots in solar cells. Transmission electron microscopy (TEM) images revealed that a multilayer structure was achieved by adjusting the thickness of the nc-SiOx layer at low temperature. Based on Raman scattering, UV-visible transmission, and steady/transient photoluminescence (PL) spectra, the microstructure, energy band, and photoluminescence properties of the films were characterized, respectively. Absorption spectra analysis indicated that the combination of the nc-Si and a-SiOx matrices affected the optical band gap of the films. The PL spectra of the multilayer films exhibited two distinct peaks as the thickness of the nc-SiOx layer was increased: a peak fixed at 1.19 eV, and another red-shifted peak near 1.45 eV. The fixed PL peak originated from radiative defects in the a-SiOx matrix, which corresponds to a PL decay life of approximately 4.6 μs. The red-shifted PL peak was attributed to a complex quantum confinement effect-defect state luminescence mechanism. This is related to two PL decay processes including a slow PL decay life, which increased from 9.9 to 16.5 μs, and a fast decay life, which was constant. The temperature-dependent PL properties further signified that the origin of the PL of the multilayer films was mainly attributed to quantum confinement effects in nc-Si.