Abstract We present a systematic study for investigating the role of exposed hydroxyapatite (HA) nanoparticles in influencing surface characteristics and mouse pre-osteoblastic MC3T3-E1 cell behavior using nanocomposites prepared by photo-crosslinking poly(ε-caprolactone) diacrylate (PCLDA) with HA. PCLDA530 and PCLDA2000 synthesized from poly(ε-caprolactone) diol precursors with nominal molecular weights of 530 and 2000 g mol −1 were used as the polymer matrices. Crosslinked PCLDA530 was amorphous while crosslinked PCLDA2000 was semi-crystalline. Crosslinked PCLDA/HA composites with different compositions of HA (10%, 20% and 30%) as well as crosslinked PCLDAs were characterized in terms of their composition-dependent physicochemical properties. The tensile, compressive and shear moduli were greatly enhanced by incorporating HA nanoparticles with the polymer matrices. The disk surfaces of original crosslinked PCLDA/HA nanocomposites were removed by cutting using a blade to expose HA nanoparticles that were embedded in the polymer substrates. The composition of HA was much higher on the cut surface, particularly in semi-crystalline crosslinked PCLDA2000/HA nanocomposites. The surface characteristics of original and cut crosslinked PCLDA/HA nanocomposites were compared and correlated with cell behavior on these nanocomposites. MC3T3-E1 cell attachment, proliferation and differentiation were significantly enhanced when the HA composition was increased in original crosslinked PCLDA/HA nanocomposites due to more bioactive HA, higher surface stiffness and rougher topography. More exposed HA on the surface of cut semi-crystalline PCLDA2000/HA nanocomposites resulted in improved hydrophilicity and significantly better MC3T3 cell attachment, proliferation and differentiation compared with the original surfaces. This study suggests that HA nanoparticles may not be fully exploited in polymer/HA nanocomposites where the top polymer surface covers the particles. The removal of this polymer layer can generate more desirable surfaces and osteoconductivity for bone repair and regeneration.