Leveraging physical factors in cellular microenvironments to promote adipose tissue-derived stem cell (ADSC) osteogenic differentiation has emerged as a new strategy in the development of scaffolds for bone tissue engineering. Anisotropicity is one of those factors of interest; however, the utilization of anisotropicity to promote ADSC osteogenic differentiation is still not efficient. In this study, we designed a substrate with a dual anisotropic structure fabricated via a combination of 3D printing and magnetic field-induced magnetic nanoparticle assembly techniques. These dual anisotropic structures have a scale hierarchy, and the scale of the magnetic nanoparticle assemblies matches that of a single ADSC. This is in contrast to conventional anisotropic osteogenic induction scaffolds that have anisotropic structures at only one scale and at an order of magnitude different from single ADSCs. ADSCs cultured on substrates with such structures have significantly higher osteogenic marker expression, e.g., ALP, at both the protein and mRNA levels, and more calcium nodule formation was also found, suggesting a stronger tendency toward osteogenic differentiation of ADSCs. RNA-seq data revealed that alterations in kinase signaling pathway transduction, cell adhesion, and cytoskeletal reconstruction may account for the elevated osteogenic induction capacity. These data support our hypothesis that such a structure could maximize the anisotropicity that ADSCs can sense and therefore promote ADSC osteogenic differentiation.