A novel flexible humidity sensor incorporating gold nanoparticles (Au NPs) and a trifunctional organosilica compound has been developed through the integration of sol–gel processing, free radical polymerization, and self-assembly techniques. The trifunctional organosilica was initially synthesized by modifying (3-mercaptopropyl)trimethoxysilane (thiol-MPTMS) with 3-(trimethoxysilyl)propyl methacrylate (vinyl-TMSPMA). Subsequently, a hydrophilic polyelectrolyte, [3(methacryloylamino)propyl]trimethyl ammonium chloride (MAPTAC), was grafted onto the MPTMS-TMSPMA gel. The Au NPs were assembled onto the thiol groups present in the MPTMS-TMSPMA-MAPTAC gel network. The compositional and microstructural properties of the Au NPs/MPTMS-TMSPMA-MAPTAC composite film were investigated utilizing Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The presence of thiol groups and mesoporous silica skeletons ensured the stability of the humidity-sensing film on the substrate under highly humid conditions, while the hydrophilic groups functioned as humidity-sensitive sites. This innovative humidity sensor demonstrated high sensitivity, acceptable linearity, minimal hysteresis, and rapid response time across a broad range of working humidity levels. Based on the complex impedance spectra analysis, hydronium ions (H3O+) were determined to govern the conductance process of the flexible humidity sensor.