Silica (SiO2) is one of the most promising inorganic nanofillers, and it has been widely used in the preparation of polymer nanocomposites due to its adjustable morphology, large specific surface area, and ease of functionalization. The surface modification, structural characteristics, and bonding mechanisms of SiO2 are crucial in enhancing the overall performance of polymer nanocomposites. This review focuses on summarizing the recent progress made regarding the preparation and structure characterization methods, unique properties, and rheological behavior of SiO2/polymer nanocomposites. In addition, the latest applications of SiO2/polymer nanocomposites in coatings, smart devices, biomedicine, and environment are further explored. A comprehensive summary of the main challenges, opportunities, and perspectives regarding SiO2/polymer nanocomposites is also presented.