There is a growing interest in developing 3D porous scaffolds with tunable architectures for bone tissue engineering. Surface topography has been shown to control stem cell behavior including differentiation. In this study, we printed 3D porous scaffolds with wavy or linear patterns to investigate the effect of wavy scaffold architecture on human mesenchymal stem cell (hMSC) osteogenesis. Five distinct wavy scaffolds were designed using sinusoidal waveforms with varying wavelengths and amplitudes, and orthogonal scaffolds were designed using linear patterns. We found that hMSCs attached to wavy patterns, spread by taking the shape of the curvatures presented by the wavy patterns, exhibited an elongated shape and mature focal adhesion points, and differentiated into the osteogenic lineage. When compared to orthogonal scaffolds, hMSCs on wavy scaffolds showed significantly enhanced osteogenesis, indicated by higher calcium deposition, alkaline phosphatase activity, and osteocalcin staining. This study aids in the development of 3D scaffolds with novel architectures to direct stem osteogenesis for bone tissue engineering.