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Surface topography and chemical characteristics can regulate stem cell proliferation and differentiation, and decrease the bone-healing time. However, the synergetic function of the surface structure and chemical cues in bone-regeneration repair was rarely studied. Herein, a strontium ion (Sr²⁺)-substituted surface hydroxyapatite (HA) hexagon-like microarray was successfully constructed on 3D-plotted HA porous scaffold through hydrothermal reaction to generate topography and chemical dual cues. The crystal phase of the Sr²⁺-substituted surface microarray was HA, while the lattice constant of the Sr²⁺-substituted microarray increased with increasing Sr²⁺-substituted amount. Sr²⁺-substituted microarray could achieve the sustainable release of Sr²⁺, which could effectively promote osteogenic differentiation of human adipose-derived stem cells (ADSCs) even without osteogenic-induced media. Osteogenic characteristics were optimally enhanced using the higher Sr²⁺-substituted surface microarray (8Sr-HA). Sr²⁺-substituted microarray on the scaffold surface could future improve the osteogenic performance of HA porous scaffold. These results indicated that the Sr²⁺-substituted HA surface hexagon-like microarray on 3D-plotted HA scaffolds had promising biological performance for bone-regeneration repair scaffold.