Using Morse potentials, we performed molecular dynamics simulations to study the effect of ZrO2/SiO2 substitution on the structure and mechanical properties of SiO2-ZrO2 glasses with various ZrO2 concentrations (5, 10, 20, 30, 40, and 50 mol%). We computed the pair distribution function (PDF) for all atomic pairs and extracted the cation-oxygen coordination number and bond distance as a function of composition for Zr4+ and other cations. We found that Zr entered the glass network as distorted [ZrO6] octahedra. Our results showed that the ZrO2 content was positively associated with the number of non-bridging oxygens and the emergence of tricluster oxygens, which consequently reduced the glass transition temperature. The elastic constants such as Young’s, bulk and shear modulus, increase with rising zirconium content.