Methylsilsesquioxane (MSQ) aerogels with uniform mesopores were facilely prepared via a sol–gel process followed by microwave drying with methyltrimethoxysilane (MTMS) as a precursor, hydrochloric acid (HCl) as a catalyst, water and methanol as solvents, hexadecyltrimethylammonium chloride (CTAC) as a surfactant and template, and propylene oxide (PO) as a gelation agent. The microstructure, chemical composition, and pore structures of the resultant MSQ aerogels were investigated in detail to achieve controllable preparation of MSQ aerogels, and the thermal stability of MSQ aerogels was also analyzed. The gelation agent, catalyst, solvent, and microwave power have important roles related to the pore structures of MSQ aerogels. Meanwhile, the microwave drying method was found to not only have a remarkable effect on improving production efficiency, but also to be conducive to avoiding the collapse of pore structure (especially micropores) during drying. The resulting MSQ aerogel microwave-dried at 500 W possessed a specific surface area up to 821 m2/g and a mesopore size of 20 nm, and displayed good thermal stability.