A phase transformation of mesoporous organosilicas from 2D-hexagonal P6mm to cubic Pm3n phase can be induced by the organotrialkoxysilane with hydrophilic pendant group with the aid of methanol during the co-condensation of 1,2-bis(trimethoxysilyl)ethane (BTME) and (EtO)(3)Si-R (R = L-prolinamide, trans-(1R,2R)-diaminocyclohexane, and gamma-aminopropyl) using the cationic surfactant, octadecyltrimethylammonium chloride (C(18)TMACl), as template in basic medium. Under similar synthesis conditions, no cubic Pm3n phase could be formed in the absence of (EtO)(3)Si-R. Depending on the type of the pendant group, different amounts of methanol were needed for the formation of the cubic Pm3n phase. N-[(triethoxysilyl)propyl]-L-prolinamide (ML-Pro) could easily induce the phase changing from 2D-hexagonal P6mm to cubic Pm3n phase probably because L-proline could result in a decreasing of the surfactant packing factor (g) through formation of large architecture on the outer boundary of the surfactant micelles. The organotrialkoxysilane can also help the formation of spherical morphology of the resultant materials.