Quantitative identification on reactive sites of target organic molecule during photocatalysis can help to get deep insight into the pollutant degradation pathway and energy evolution process. In this study, a new class of silica aerogel supported TiO2 (TiO2/SiO2) photocatalysts were fabricated via a two-step approach, and applied for adsorption and photocatalytic degradation of phenanthrene. Anatase crystalline structure was formed upon calcination at 400 and 600 °C, while mixed crystal interphases of anatase and rutile were generated at 800 °C (anatase:rutile = 0.67:0.33). The higher calcination temperature resulted in better crystallinity of TiO2, higher photocatalytic activity, and reduced adsorption affinity toward phenanthrene. TiO2/SiO2-800 (TiO2/SiO2 calcined at 800 °C) showed minimal phenanthrene uptake (~5.2%) but the strongest photocatalytic activity, and it was able to completely degrade phenanthrene within 3 h. The SiO2 aerogel component in the composite enabled the pre-concentration of phenanthrene on the photoactive sites, while the nanoscale mixed-phases of anatase and rutile of TiO2/SiO2-800 act as an efficient transfer medium for photo-induced charge carriers. Moreover, the formed Ti–O–Si linkage in TiO2/SiO2-800 induced formation of Ti3+ under solar light irradiation, promoting photoexcited electron trap and separation of electron-hole pairs. Based on the degraded phenanthrene intermediates/products, theoretical calculations according to the density functional theory (DFT) reveal that the atoms of phenanthrene with high electrophilic Fukui index (f-) are the most reactive sites towards the radicals. Potential energy surface profile for phenanthrene degradation further reveals the intermediates energy evaluation via radicals attack.