This study aims to investigate the surface characterization and pre-osteoblast biological behaviors on the three-dimensional (3D) poly(ε-caprolactone)/β-tricalcium phosphate (β-TCP) scaffold modified by amine plasma-polymerization. The 3D PCL scaffolds were fabricated using fused deposition modeling (FDM) 3D printing. To improve the pre-osteoblast bioactivity, the 3D PCL scaffold was modified by adding β-TCP nanoparticles, and then scaffold surfaces were modified by amine plasma-polymerization using monomer allylamine (AA) and 1,2-diaminocyclohexane (DACH). After the plasma-polymerization of PCL/β-TCP, surface characterizations such as contact angle, AFM, XRD, and FTIR were evaluated. In addition, mechanical strength was measured by UTM. The pre-osteoblast bioactivities were evaluated by focal adhesion and cell proliferation. Osteogenic differentiation was investigated by ALP activity, Alizarin red staining, and Western blot. Plasma-polymerization induced the increase in hydrophilicity of the surface of the 3D PCL/β-TCP scaffold due to the deposition of amine polymeric thin film on the scaffold surface. Focal adhesion and proliferation of pre-osteoblast improved, and osteogenic differentiation was increased. These results indicated that 3D PCL/β-TCP scaffolds treated with DACH plasma-polymerization showed the highest bioactivity compared to the other samples. We suggest that 3D PCL/β-TCP scaffolds treated with DACH and AA plasma-polymerization can be used as a promising candidate for osteoblast differentiation of pre-osteoblast.