The hierarchical three-dimensional (3D)-printing scaffolds based on microbial polyester poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P34HB) were designed and used for bone tissue engineering via surface functionalization on 3D-printed (P34HB) scaffolds using polydopamine (PDA)-mediated recombinant human bone morphogenetic protein-2 (BMP2), leading to enhanced bone formation in a rat model with a calvarial critical-size bone defect. Taking advantage of the adhesive property of PDA under alkaline and aerobic conditions, osteogenic BMP2 was captured on the surface of PHA scaffolds, resulting in their enhanced osteogenic bioactivity, better stem cell adhesion and proliferation, and sustainable release of a bioactive substance over a period of 30 days. These contributed to notable differences in alkaline phosphatase (ALP) activity, mineralization, expressions of osteogenesis-related genes, as well as finally enhanced in vivo bone formation in rats. The functionalized 3D-printed P34HB scaffolds via the PDA-mediated osteogenic activity were developed as a versatile platform for bone tissue regeneration.