Porous materials are of great importance in many fields due to their wide applications. An ongoing theme in this area is the tailoring of materials for specific applications. With a better understanding of the formation mechanisms, tailoring and controlling the pore structure may be achieved. The objective of this research is acquiring further understanding of the fundamental physics that govern the formation of these materials using molecular simulations. We are aiming to unravel the assembly process of silica porous materials using a semi-rigid silica tetrahedral model. This model together with reaction ensemble Monte Carlo simulations allows us to study the formation of silica nanoparticles, the initial stages of microporous material formation. A two-step formation mechanism was found to be crucial for generating the nanoparticles. A replica-exchange reaction ensemble Monte Carlo sampling together with the silica tetrahedral model is developed and applied to cross the energy barrier between amorphous silica to crystalline silica materials for searching for the ground state structure of this model. The technique involves simulating several system copies with different equilibrium constants controlling silica condensation/hydrolysis reactions, which are essential for building higher-order network structures and eventually crystals, was preformed. Different silica polymorphs including all-silica zeolite frameworks were obtained. This model shows a great potential to study the crystallization of microporous materials. We also study the formation of mesoporous materials using molecular dynamics simulations. We investigate the interplay of silica molecules and surfactants, and different mesophases such as micellar rods, hexagonal, bicontinuous and lamellar phases were obtained. Multiple charges on silicate oligomers were found to play an important role in the formation of hexagonal phases. To study the later stages of MCM-41 formation, a hybrid molecular dynamics and Monte Carlo approach is proposed. The cooperation between the physical interaction and chemical reaction can be taken into account simultaneously. Preliminary study shows that the ratio of silicate to surfactant higher than 4 is essential to the growth of MCM-41. With a further enhancement on the model, this hybrid approach will be a powerful tool to simulate the formation of MCM-41 in a large system and at a long time scale.