Fabrication of scaffolds for bone tissue engineering applications often involves the use of two distinct classes of calcium-containing biomaterials, namely calcium phosphates and calcium silicates. The selection of these materials is based on their biocompatibility and bioactivity. Although these bioceramics are very similar to natural bone from the point of view of mineral compounds, unlike bone, they are brittle. The current research examines the use of hydroxyapatite and tricalcium silicate, which are the most common calcium phosphates and calcium silicates, in the field of bone scaffold applications, respectively. The present study shows the effect of different concentrations of ceramic nanoparticles when combined with sodium alginate hydrogel on the construction of bone scaffolds by molecular dynamics simulation. Stability and self-assembly have been evaluated through several parameters such as solvent-accessible-surface-area, radius of gyration, radial distribution function, root mean square deviations, hydrogen bonding, van der Waals energy, electrostatic energy, and total energy. The simulation results show that the addition of 10% by weight of hydroxyapatite and tricalcium silicate to the sodium alginate hydrogel matrix leads to the formation of a more compact, stable, and less hydrated structure and can potentially affect the mechanical properties of the scaffold and its interaction with Cells help. The findings of this research show that tricalcium silicate samples have superior properties for making scaffolds compared to hydroxyapatite samples, especially in terms of combination with sodium alginate hydrogel. However, it is necessary to conduct experimental tests to confirm the results of the simulations.