Surface microstructure of implant materials is an essential factor for soft tissue healing around the implant. The purpose of this study was to explore the effect of different microchip surface microstructures on the adhesion and proliferation of cells and bacteria. Hydroxyapatite (HA) microchips with different microstructures (linear, decussate, circular and triangular) and their polydimethylsiloxane (PDMS) replica chips were prepared. Myoblast cells (C2C12), Staphylococcus aureus and Porphyromonas gingivalis were seeded on these chips to investigate the effect of different surface microstructures on the adhesion and proliferation. The results indicated that different surface microstructure in the same size did not show much difference on adhesion and proliferation of cell and bacteria; compared to microstructure region (grain ca. 2 μm), the cells preferred to adhesion and proliferate in the blank area (grain ca. 260 nm), in contrast, the bacteria were significantly preferable to the microstructure regions. In conclusion, it might be better for the implant materials to be manufactured in submicron-scale rather than micro-scale to improve the proliferation of cells and to inhibit the adhesion and growth of bacteria.