The concentration of the binder is a key factor affecting the quality of 3D-printed bone scaffolds. This study analyzed the influence of polyvinyl alcohol (PVA) aqueous solution concentration on the properties of hydroxyapatite (HA)/β-tricalcium phosphate (β-TCP) bone scaffolds from both microscopic and macroscopic perspectives using molecular dynamics (MD) simulations and experimental research. In the MD simulations, the changes in chain length corresponding to different concentrations were used to analyze the microscopic interactions between PVA and the powder material system. In the experiments, the solid content, zeta potential, and extrusion rheological properties of the slurry were analyzed under PVA concentrations ranging from 5% to 15% by mass. Bone scaffolds were then fabricated using 3D printing and freeze-drying processes, and the changes in porosity, mechanical properties, dimensional shrinkage, and swelling effect of the scaffolds were examined. Finally, the biological properties of the scaffolds were verified through in vitro experiments. The results showed that the hydrogen bonds and ionic bonds formed between PVA and the powder materials are the main forces for adhesion, and the increase in chain length, which leads to an increase in Cauchy pressure, enhances the basic mechanical properties of the material. Slurries with higher PVA concentrations have higher solid content and shear-thinning capabilities, ensuring better printability, and the resulting bone scaffolds exhibit higher mechanical properties and drying shrinkage characteristics. However, this also leads to lower porosity and swelling rates. In vitro experiments revealed that an increase in PVA aqueous solution concentration results in decreased porosity and ion concentration of the bone scaffolds, thereby reducing their bioactivity. The conclusions drawn from this study can be used to predict the performance of slurries and bone scaffolds at different binder concentrations, providing a theoretical basis for the selection of binder concentration in 3D-printed bone scaffolds.