The characteristics of nano-crystalline silicon (nc-Si) embedded in Si-based dielectric matrix have been investigated extensively. However, these Si-based dielectric materials have the highly-resistive nature and difficulty in building up the built-in electric field, which limit the performances of nc-Si thin films for solar cell (SC) application. In this study, we propose to use ZnO as a new matrix material for the nc-Si thin films with better optoelectronic properties because of the unique characteristics of ZnO. We successfully demonstrate the formation of nc-Si embedded in ZnO thin films using a ZnO/Si multilayer (ML) structure by radio-frequency (RF) magnetron sputtering method. From the high-resolution transmission electron microscope (HRTEM) images, we clearly observe the amorphous Si (a-Si) nano-clusters after deposition and high density of nano-crystalline clusters after annealing in the ZnO/Si ML structure. From atomic force microscope (AFM) images, significant variations on the surface morphologies are observed under different Si sputtering powers (P Si) after deposition. The larger surface roughness and clearer formation of a-Si nano-clusters are observed for P Si higher than 75 W. Combined with the Raman spectra and X-ray diffraction patterns, the results indicate that the sputtered Si atoms with higher P Si have more kinetic energy to aggregate together and are easier to form a-Si nano-clusters during deposition. Such morphology is helpful for the nc-Si formation and the better crystallization of the ZnO matrix during annealing. Thus, high density of nano-crystalline clusters is observed in the HRTEM images after annealing. Our experimental results show the nc-Si embedded ZnO thin film is certainly achievable, and a high conversion efficiency SC integrating nc-Si thin film with ZnO matrix can be expected.