Structure and physical properties of monolithic polymethylsilsesquioxane (PMSQ, CH3SiO1.5) aerogels have been systematically examined with varied starting compositions using a sol–gel system containing surfactant n-hexadecyltrimethylammonium chloride (CTAC). The precursor methyltrimethoxysilane (MTMS) undergoes hydrolysis and polycondensation under an acid–base two-step reaction to obtain uniform gels as a one-pot reaction. To compare the samples, each factor of starting composition, such as amount of CTAC, concentration of aqueous acetic acid solution, volume of solvent and amount of urea, is independently varied. With appropriate concentrations of surfactant CTAC, the aerogels with high light transmittance (at 550nm) are obtained, owing to the effective suppression of macroscopic phase separation. Acid–base catalysts, acetic acid and urea also impose significant effects on the properties of obtained aerogels including their molecular-level structures. The aerogel with 91% of light transmittance was obtained under an optimized condition. The lowest density of the PMSQ aerogel in this system reaches 0.045gcm−3.