Nanoporous silica systems with porosity between 30% and 70% were developed using two Molecular Dynamics (MD) simulation protocols to obtain structures with dissimilar pore morphologies. Short- and medium-range structural characteristics including bond angle distributions and pair distribution functions were analyzed and found to be consistent with experimental results. Surface area to volume ratio and pore microstructures were characterized and compared with experimental observations. Mechanical properties including elastic, shear, and bulk moduli of these nanoporous silica systems were calculated and their change as a function of porosity was compared with experimental data and theoretical models. It was found that the elastic modulus of porous silica with 50% porosity is 5–14 GPa which is consistent with experimental results. The elastic moduli–porosity relationship was fitted by exponential and power functions, and analysis of coefficients was performed to obtain microstructure characteristics of the simulated nanoporous silica structures. This works confirms that two distinct nanoporous silica microstructures are generated with MD simulations which result in variations in mechanical properties and highlight the importance of selecting a nanoporous silica simulation method which approximates experimental systems.