Moisture-induced damage is one of the primary causes of premature distress in asphalt pavements, leading to reduced service life and increased maintenance costs. Although nanomaterials have shown potential in enhancing asphalt performance, the underlying composite interaction mechanisms among nanomaterials, asphalt binder, and aggregate phases under moisture exposure are still not fully understood. In addition, comparative evaluations under consistent experimental conditions remain limited. This study investigates the influence of five nanomaterials: nano-silica (NS), nano-alumina (NA), nano-titanium dioxide (NT), nano-zinc oxide (NZ), and carbon nanotubes (CNT) on the physical and mechanical properties of asphalt binders and mixtures, with particular emphasis on moisture damage resistance. The nanomaterials were incorporated at dosages of 1.5%, 3.0%, 4.5%, and 6.0% by binder weight. Binder performance was evaluated using conventional and performance grading (PG) tests, while mixture performance was assessed through Marshall properties and moisture susceptibility indicators, including the tensile strength ratio (TSR) and the index of retained strength (IRS). Fluorescence microscopy (FM), scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR) were employed to investigate nanomaterial dispersion characteristics, microstructural morphology, and physicochemical interactions within the asphalt composite system. The results indicate that nanomaterial modification reduced penetration and increased softening point and Marshall stability, reflecting enhanced stiffness and thermal resistance, although ductility decreased at higher dosages. Significant improvements in moisture resistance were observed, particularly under conditioned states. The TSR increased from 81.2% for the control mixture to 92.4% for NS and 91.7% for NA, while the IRS improved from 72.7% to 88.5% for NS. Statistical analysis indicated that both nanomaterial type and dosage significantly affected TSR and IRS performance, with dosage exhibiting comparatively greater influence on moisture resistance improvement. FM and SEM analyses revealed comparatively better dispersion and lower agglomeration tendency for NS and NA, which corresponded to their superior moisture resistance performance. FTIR analysis indicated that the modification process was predominantly physical, with no major formation of new chemical functional groups. Among the investigated nano materials, NS at 6% dosage exhibited the most pronounced improvement, followed by NA at similar dosage levels. Overall, the findings suggest that nanomaterial modification can considerably improve the moisture resistance and mechanical performance of asphalt mixtures under laboratory conditions. However, higher nanomaterial dosages may adversely affect binder workability due to increased viscosity, particularly in CNT-modified binders.