The design of nano- and microstructures based on self-organization is a key area of research in the search for new biomaterials, and such structures have a variety of potential applications in tissue engineering scaffolds. We have reported a honeycomb-patterned polymer film (honeycomb film) with highly regular pores that is formed by self-organization. In order to utilize the honeycomb film as a scaffold for bone tissue engineering, hydroxyapatite (HA) was formed on the honeycomb film. In this study, we prepared a 3D scaffold comprising HA and a poly(ɛ-caprolactone) honeycomb film in a simulated body fluid (SBF) by changing the degree of hydrophilicity of the film. We investigated the dependence of the amount of HA formed on the length of time for which hydrolysis and soaking in SBF were carried out. Further, we characterized the crystallinity of the HA thus formed. We clarified that the amount of HA formed and its crystallinity were controlled by the length of time for which hydrolysis and soaking of the film were carried out. These HA-deposited honeycomb films, which have the HA microstructure, could serve as a novel scaffold for bone tissue engineering.