The effects of post-synthesis treatments on the structure and the stability of MCM-41 mesoporous material were investigated. It was found that, by adding ammonium salts and adjusting pH during the post-synthesis to alkalescently synthesized MCM-41, the regularity of the pore was improved dramatically and the stability of the mesostructure was retained; conversely, they were diminished by adding sodium salts. The results were studied by analyzing the samples using X-ray diffraction (XRD), Transmission electron microscopy (TEM), Differential Thermal Analysis–Thermal Gravimetry (DTA–TG). The change of the electrostatic surrounding and the formation of hydrogen bonds caused by different ions were confirmed to be the main factors.