We fabricated surface nanostructures with different pillar and cone shapes on glass substrates using thermally dewetted gold (Au) nanoparticles as etch masks by dry etching. Their optical total transmittance characteristics, together with theoretical predictions using rigorous coupled-wave analysis simulation, and wetting behaviors were investigated. The nanostructured glass substrates strongly enhanced the surface transmission compared to the flat glass substrate. The glass nanocones with a linearly graded effective refractive index profile exhibited better transmission properties than the glass nanopillars due to the lower surface reflectance, thus leading to higher average transmittance with increasing their height. For the glass nanocones with a period of 106 ± 39 nm at the Au film thickness of 5 nm, the higher average total transmittance (Tave) and solar weighted transmittance (SWT) of ~95.5 and ~95.8% at wavelengths of 300-1100 nm and the lower contact angle (θc) of 31° were obtained compared to the flat glass substrate (i.e., Tave~92.7%, SWT~92.7%, and θc~65°). The calculated total transmittance results showed a similar tendency to the experimental results.