Osteoarthritis (OA) is a disease that leads to the damage of subchondral bone. To treat OA, patients can have surgery to implant biomaterials into the damaged area. In this research, biomaterials of 3D porous scaffolds were fabricated by the use of air microbubbles for subchondral bone formation proposed for OA surgery. Microbubbles were generated in a polyvinyl alcohol solution at various air flow rates of 20 (F20), 100 (F100), 200 (F200), and 300 (F300) cc min−1. Molecular organization, structure, and morphology of the scaffolds were characterized and observed by Fourier transform infrared spectroscopy, a differential scanning calorimeter, and a scanning electron microscope, respectively. Physical and mechanical properties based on swelling behavior and compressive strength of the scaffolds were also evaluated. Biological performance by means of osteoblast proliferation, protein synthesis, and alkaline phosphatase activity of the scaffolds were studied. The scaffolds showed molecular organization via interaction of –OH and C = O. They had residual water in their structures. The scaffolds exhibited a morphology of a spherical-like cell shape with small pores and a rough surface produced on each cell. Each cell was well connected with the others. The cell size and porous structure of the scaffolds depended significantly on the flow rate used. The molecular organization, structure, and morphology of the scaffolds had an effect on their physical and mechanical properties and biological performance. F100 was found to be an optimum scaffold offering a molecular organization, structure, morphology, physical and mechanical properties, and biological performance which was suitable for subchondral bone formation. This research deduced that the F100 scaffold is promising for OA surgery.