Sol–gel synthesis of macroporous polymethylsilsesquioxane (PMSQ) monoliths has been successful over the past decade, and applications to separation media have been investigated. However, the control of mesopores to tailor hierarchical porosity, which is promising for improvement of the separation efficiency, remains challenging. In particular, an independent control of meso- and macropores has not been achieved in PMSQ. Herein we present a method to synthesize PMSQ monoliths with well-defined macropores and controlled mesostructure (pore size ranging from 10 to 60 nm, total pore volume from 0.2 to 0.6 cm³ g⁻¹) via sol–gel accompanied by phase separation. Different Pluronic-type nonionic surfactants were used to control phase separation of the hydrophobic PMSQ network in aqueous media. Due to different packing density of the colloidal PMSQ constituents in the continuous skeletons in the micrometer-scale (termed as macropore skeletons) and their rearrangements through the hydrothermal post-treatment under basic conditions, mesopore characteristics have been successfully controlled independently of the preformed macropore structure. Separation columns for high-performance liquid chromatography (HPLC) have been fabricated using the PMSQ monoliths, and acceptable separation performances in both the reversed-phase and normal-phase modes have been demonstrated due to the presence of both hydrophilic silanol groups and hydrophobic methyl groups.