Phase-separated siloxane gels with co-continuous porous structures in the length scale from nanometers to micrometers have been synthesized in confined spaces especially in short cylindrical pores within porous medium. Morphology of the phase-separated gels derived from both methyltrimethoxysilane (MTMS) and tetramethoxysilane (TMOS) inside the porous medium was significantly affected by preferential wetting by siloxane phase on the internal surface of the mold. When spinodal wavelength of the guest gel becomes larger than pore size of the porous medium, wetting transition has been observed in the systems with strong affinity between siloxane phase and the internal surface of the mold.