Silica is the most abundant mineral in the crust of the Earth. It has been demonstrated that the aluminum concentration in silica plays a key role in determining many properties of silica-based components. Although the alumina-silica system has been intensely studied, the effect of very small amounts of aluminum on the structure and properties of silica remains unclear. We report results of first principles calculations showing that small amounts of aluminum could be metastable when located in the center of Si-O rings without breaking the silica network. In contrast, higher aluminum contents will result in the destruction of the Si-O bonds, leading to the formation of triclusters and a 4-, 5-, and 6-fold Al-O coordination, as observed in previous studies. Based on the silica structure obtained through geometric optimization, the properties of silica doped with small amounts of aluminum were calculated. The results can account for many ‘abnormal’ phenomena experimentally observed. The results benefit most areas such as geosciences, microelectronics, glass industry, and ceramic materials.