Silica reagents are expensive and toxic for use in the synthesis of mesoporous silica materials. It is imperative to take an interest in green silicon sources. In this paper, we report the synthesis of hexagonal and ordered aluminum-containing mesoporous silica materials (Al–MCM–41) from natural perlite mineral without addition of silica or aluminum reagents. A pretreatment process involving acid leaching, alkali leaching, and strongly acidic cation exchange resins treatment was critical to obtain silicon and aluminum sources from natural perlite mineral. The Al–MCM–41 material was synthesized via a hydrothermal reaction with hexadecyl trimethyl ammonium bromide (CTAB) as the template and subsequent calcination. The resulting mesophase had a hexagonal and ordered mesoporous structure, confirmed by small-angle X-ray diffraction (SAXRD) and transmission electron microscopy (TEM). Al–MCM–41 material had a high Brunauer–Emmet–Teller (BET) surface area of 1024 m2/g, pore volume of 0.72 cm3/g and an average pore diameter of 2.8 nm with a pore size distribution centered at 2.5 nm. The thermal behavior of the as-synthesized samples during calcination was investigated by thermogravimetry (TG) and differential thermogravimetry (DTG) analysis. The Al–MCM–41 material showed a negative surface charge in aqueous solution with the pH value ranging from 2 to 13. The variations of chemical structures from natural perlite to Al–MCM–41 were traced by wide-angle X-ray diffraction (WAXRD) and Fourier-transform infrared spectroscopy (FTIR). A proposed mechanism for the synthesis of hexagonal and ordered mesoporous silica materials from natural perlite is discussed.