Methylsilsesquioxane aerogels with uniform mesopores have been facilely prepared via a sol–gel process followed by microwave drying with methyltrimethoxysilane (MTMS) as precursor, hydrochloric acid (HCl) as catalyst, water and methanol as solvents, hexadecyltrimethylammonium chloride (CTAC) as surfactant and template and propylene oxide (PO) as 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 on pore structures of MSQ aerogels. Meanwhile, microwave drying method is found to not only have a remarkable effect on improving production efficiency, but also be conducive to avoid the collapse of pore structure especially micropores during drying. The resulting MSQ aerogel microwave-dried at 500 W possesses a specific surface area up to 821 m2/g and a mesopore size of 20 nm, and displays good thermal stability.