This study conducts a deeper analysis of mortar’s mechanical and microstructural characteristics by examining the influence of nano-silica derived from fly ash on mortar’s compressive strength and microstructure using the ratios of water-to-cement (w/c) of 0.40, 0.45, and 0.485. Nano-silica was synthesized via the sol–gel method, yielding amorphous spherical particles ranging from 30 to 80 nm in size, with 98.37% SiO₂ content, as observed from SEM micrographs. XRD patterns revealed a broad peak at 2θ ≈ 22°, confirming the amorphous nature of the synthesized silica. FTIR spectra exhibited characteristic Si–O–Si and Si–OH vibrations at 1080 cm⁻¹ and 950 cm⁻¹, respectively, verifying the presence of silica networks. Mortar mixtures contained nano-silica ranging from 1%, 2%, 3% and 4% by cement weight and were tested after 28 days of curing. The highest compressive strength was achieved with 1% nano-silica at w/c = 0.40, showing more than a 29% increase compared to the control sample. Unlike prior studies, this work integrates compressive strength, SEM, XRD, and FTIR analyses in a single investigation of fly ash-derived nano-silica under varying w/c ratios. Additionally, XRD and FTIR analyses indicated increased C–S–H formation and hydration level, while SEM showed a denser matrix with fewer pores. The results highlight that the optimal nano-silica content improves mortar performance and promotes the sustainable use of industrial waste. Overall, nano-silica derived from fly ash effectively enhances the microstructure and mechanical performance of mortar by promoting C–S–H gel formation and densifying the interfacial transition zone. This study provides new insight into the potential of fly ash waste valorization for producing functional nanomaterials in sustainable cementitious systems.