Bioactive glasses (BGs) have been considered as one of the important materials in medical and tissue engineering (TE) applications. Understanding the structure of BGs is very important factor for predicting their properties, hence molecular dynamics (MD) simulation is a suitable method to investigate the properties of BGs along with experimental investigations. Therefore, in this study, the short-range, medium-range and long-range structures of 50SiO₂-50CaO and 60SiO₂-40CaO bioactive glasses were studied using MD simulation, and the self-diffusion coefficients were also calculate using the mean square displacement (MSD) of atoms. To study the short-range structure, the bond length of Si-O, Ca-O and O-O bonds of 50SiO₂-50CaO BG were investigated and reported 1.615 ± 0.010, 2.385 ± 0.010 and 2.625 ± 0.010, respectively. Meanwhile, 1.615 ± 0.010, 2.375 ± 0.010 and 2.635 ± 0.010 were reported for 60SiO₂-40CaO BG, respectively. To study the medium-range structure, the coordination number (CN) of atoms, the distribution of bridging and non-bridging oxygens (NBO), and the distribution of Qⁿ were studied and their relationship with bioactivity was investigated. Additionally, the density of BGs was investigated and 2.47±0.01 g/cm³ and 2.61±0.01 g/cm³ were reported for 50SiO₂-50CaO and 60SiO₂-40CaO, respectively. Moreover, the self-diffusion coefficients (SDCs) of atoms were investigated at 1500 and 2000 ⁰K temperatures and results indicated that SDC of atoms increase with increasing the temperature. The results for the short-range structure were validated using the previous reports, and the bioactivity of 50SiO₂-50CaO and 60SiO₂-40CaO were compared with each other. It was found that 50SiO₂ -50CaO BG is more degradable and 60SiO₂-40CaO had more hydroxyapatite (HA) formation capability. Eventually, considering the aforementioned properties, these two BGs can be used in TE applications.