The photocatalytic activity of eco-friendly zinc oxide doped silica nanocomposites, synthesized via a co-precipitation method followed by heat-treatment at 300, 600, and 900 °C is investigated. The samples have been characterized by employing X-ray diffraction method, and further analyzed using the Rietveld Refinement method. The samples show a space group P63mc with hexagonal structure. The prepared composites are tested for their photocatalytic activities for the degradation of methyl orange-based water pollutants under ultra-violet (UV) irradiation using a 125 W mercury lamp. A systematic analysis of parameters such as the irradiation time, pH value, annealing temperatures, and the concentration of sodium hydroxide impacting the degradation of the methyl orange (MO) is carried out using UV-visible spectroscopy. The ZnO.SiO₂ nanocomposite annealed at 300 °C at a pH value of seven shows a maximum photo-degradation ability (~98.1%) towards methyl orange, while the photo-degradation ability of ZnO.SiO₂ nanocomposites decreases with annealing temperature (i.e., for 600 and 900 °C) due to the aspect ratio. Moreover, it is seen that with increment in the concentration of the NaOH (i.e., from 1 to 3 g), the photo-degradation of the dye component is enhanced from 20.9 to 53.8%, whereas a reverse trend of degradation ability is observed for higher concentrations.