The effect of Al substitution on the hydrothermal stability of Si-Al-MCM-41 (Si/Al = 50) under different treatment conditions has been investigated in detail, and a fundamental understanding is discussed based on its effect on both geometrical and chemical properties of MCM-41. Compared with Si-MCM-41, the small amount of Al substituted in the framework of Si-Al-MCM-41 is shown to give remarkable improvement of the hydrothermal stability of Si-Al-MCM-41 in boiling water for days. It is found that the existence of Al and Na species in Si-Al-MCM-41 yields less uniformly arranged pare structures than Si-MCM-41, providing a better hydrothermal stability for Si-Al-MCM-41. Both the Al in the framework and the nonstructural Al species on the surface help to protect the mesoporous structure from degradation in boiling water. In addition, the presence of TEAOH during the synthesis of Si-Al-MCM-41 may result in a better condensation of the Si-O-Si bonds, enhancing the stability of Si-Al-MCM-41 under the hydrothermal treatment conditions.