The mechanism of the gel formation process has been studied using molecular dynamics (MD) simulation. Two characteristic systems considered are silicic acid, Si(OH)(4), and monomethoxy silicic acid, Si(OMe)(OH)(3), which are regarded as differing from each other in the extent of hydrolysis. The interatomic potential used is that of Feuston and Garofalini [B.P. Feuston, S.H. Garofalini, J. Phys. Chem., 94 (1990) 5351-5356.], except for a slight modification about methoxy groups. Microscopic features of the structural development are discussed. There is a slow cluster growth during the early stage, a rapid cluster growth follows this due to cluster-cluster aggregation, and the network structure becomes denser with time through the repeated bond-formation and bond-breaking. Finally, the trend of phase separation is observed. The presence of the methoxy groups interferes with the aggregation and the formation of the dense network structure. Having some problems to be examined about set temperature, system size and dilution effect, MD simulation has proved effective for understanding the structural development in sol-gel process for silica systems.