Surface acoustic wave (SAW) technology has been widely developed for ultraviolet (UV) detection due to its advantages of miniaturization, portability, potential to be integrated with microelectronics, and passive/wireless capabilities. To enhance UV sensitivity, nanowires (NWs), such as ZnO, are often applied to enhance SAW-based UV detection due to their highly porous and interconnected 3D network structures and good UV sensitivity. However, ZnO NWs are normally hydrophilic, and thus, changes in environmental parameters such as humidity will significantly influence the detection precision and sensitivity of SAW-based UV sensors. To solve this issue, in this work, we proposed a new strategy using ZnO NWs wrapped with hydrophobic silica nanoparticles as the effective sensing layer. Analysis of the distribution and chemical bonds of these hydrophobic silica nanoparticles showed that numerous C-F bonds (which are hydrophobic) were found on the surface of the sensitive layer, which effectively blocked the adsorption of water molecules onto the ZnO NWs. This new sensing layer design minimizes the influence of humidity on the ZnO NW-based UV sensor within the relative humidity range of 10–70%. The sensor showed a UV sensitivity of 9.53 ppm (mW/cm2)−1, with high linearity (R2 value of 0.99904), small hysteresis (<1.65%) and good repeatability. This work solves the long-term dilemma of ZnO NW-based sensors, which are often sensitive to humidity changes.