Polycaprolactone (PCL) is one of the most widely used 3D printing materials with good biocompatibility and mechanical properties, but its hydrophobic properties are detrimental to cell adhesion and proliferation. Studies have shown that polydopamine (PDA) promotes the proliferation and induces osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) on the polymer surface. However, the effect of different PDA coating thicknesses on the osteogenic differentiation of BMSCs has rarely been reported. In this paper, PCL scaffolds were prepared using 3D printing technology, and PCL scaffolds with PDA surface coating (PDA-PCL-0, PDA-PCL-3, PDA-PCL-6, PDA-PCL-24) were obtained after immersing them in aqueous dopamine solution for fixed time points by shaking bed shaking (0h, 3h, 6h, 24h). The scaffolds of each group were subjected to characterization analysis and physicochemical performance tests to evaluate the differences in the scaffolds' BMSCs-promoting proliferation, adhesion and osteogenic properties. The results showed that the PDA-PCL-6 possessed immunomodulatory properties and significantly promoted the proliferation and adhesion of BMSCs as well as osteogenic differentiation compared with other groups. In the validation experiments in vivo, based on the results of mCT, H&E staining, Masson staining and immunohistochemical staining (BMP-2 and COL-1), the coated scaffolds (PDA-PCL-6) showed significant bone regeneration-promoting properties, as well as good histocompatibility and haemocompatibility, compared with the scaffolds without PDA coating at 1, 2, and 3 months after the operation. In conclusion, our results indicate that the PDA coating obtained by immersion for 6 hours significantly enhances the biocompatibility and osteoinduction of PCL, providing a promising strategy for bone defect repair.