Macroporous methylsilsesquioxane (MSQ) monoliths have been prepared by in situ two-step processing using an initial acid catalysis step accompanied by an epoxide-mediated condensation step in the presence of ammonium chloride (NH4Cl). We investigate the effects of duration time of acidic step, heat-treatment and hydrothermal treatment on the macroporous morphology and pore structures of MSQ monoliths. The duration time of acidic step gives an important effect on the macroporous morphology and pore structures of MSQ monoliths, resulting from the polymerization of MSQ. Heat-treatment and hydrothermal treatment basically do not spoil the macroporous morphology of MSQ monoliths, while obviously varies the mesopore/micropore structures including pore size, pore volume, and pore size distribution. The macroporous MSQ materials with thick skeleton and intrinsic hydrophobicity are promising for wide applications such as ultra performance liquid chromatography (UPLC), superhydrophobic materials and so on.