<p>Successful bone tissue engineering using 3D-porous scaffolds is hampered by insufficient oxygen diffusion and non-uniform cell distribution, which are determined by cell culture parameters. Here we aimed to investigate the influence of cell culture parameters on oxygen diffusion and cell distribution in 3D-porous scaffolds during 15-days by finite-element (FE) modeling. Osteosarcoma cells were cultured in 3D-porous silk scaffolds under 0.05, 0.12, and 0.2&#xa0;mol/m³ medium-oxygen to validate FE modeling. Oxygen concentration in scaffolds decreased by enhancing initial cell number seeded, medium-oxygen concentration, and maximum specific cell growth rate, while it increased by enhancing cell motility-coefficient and molecular diffusivity of oxygen-in-the-cell-phase. Cell density increased by enhancing medium-oxygen concentration, maximum specific cell growth rate, cell motility-coefficient, and molecular diffusivity of oxygen-in-the-cell-phase, while it decreased by enhancing initial cell seeding number. The FE modeling results of cell proliferation in scaffolds were not significantly (&lt; 8%) different from experimental results, indicating that FE modeling data were in good agreement with experimental results. In conclusion, initial cell number seeded, medium-oxygen concentration, and maximum specific cell growth rate, but not cell motility-coefficient or molecular diffusivity of oxygen-in-the-cell-phase, are crucial for creating densely cell-populated constructs with uniform cell distribution in 3D-porous scaffolds, informing future scaffold-based bone regeneration strategies.</p> Graphical Abstract <p></p>