The orientation of the c-axis in octacalcium phosphate (OCP) nanocrystals that were incorporated into hybrid thin films was successfully tuned using poly(vinyl alcohol) (PVA) thin-film templates of varying thicknesses. This approach was inspired by biomineralization. Thicker PVA templates enhanced the c-axis orientation of the OCP crystals perpendicular to the substrate. Using this approach with a 900 nm thick PVA template, OCP/PVA hybrid thin films (1.8 μm thick) with a c-axis orientation perpendicular to the substrate were formed. Hydroxyapatite (HAP) hybrid thin films that also exhibited a perpendicular c-axis orientation were obtained through the topotactic transformation of the OCP/PVA hybrid thin films in aqueous solution. The thickness change of the polymer templates had a significant effect on the structure of the OCP nanocrystals in the hybrid thin films. The structural control of the OCP hybrid thin films that were formed through the biomineralization-inspired approach allowed the formation of HAP hybrid thin films with controlled structures.