In this paper, we report the successful synthesis of amine-functionalized FDU-12-type mesoporous silica with a very large pore (30.2 nm) and a highly ordered mesostructure by using 3-aminopropyltriethoxysilane (APTES) as an organosilane source. Small angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) measurements confirmed that the materials possessed a face-centered cubic (space group Fm3m) mesostructure. Different techniques were used to obtain a significant pore and entrance size enlargement: low synthesis temperature and high hydrothermal treatment temperature. The amount of amine organosilane influenced the mesostructure of the mesoporous silica. It was found that the addition of inorganic salt (KCl) could help to maintain an ordered structure of the large pore mesoporous material. X-ray photoelectron spectroscopy (XPS), solid-state magic-angle spinning (MAS) 13C nuclear magnetic resonance (NMR) and thermogravimetric analysis (TGA) verified the incorporation of amine functional groups on the surface of the materials. The addition of amine organosilane extended the synthesis temperature domain of ordered FDU-12 materials. The amine functional group significantly enhanced the adsorption capacity of the mesoporous materials, e.g., the amine functionalized mesoporous silica had 8-fold higher bovine serum albumin (BSA) adsorption capacity than that of the unfunctionalized one. It also had 2 times higher adsorption capacity for large cellulase enzymes. The amine functional group introduced positively charged groups on the surface of the mesoporous silica, which created strong electrostatic interactions between the protein and the silica.