To develop an improved surface conformation of titanium web (TW) scaffold, we examined the in vitro and in vivo biocompatibility of a thin hydroxyapatite (HA) deposited by pulsed laser ablation. Thin HA film was deposited on titanium discs using an pulsed laser operating at a repletion rate of 10 Hz and annealed by heating at 380 °C for 1 h. The presence of HA not only along the surface but also in the TW inner region was confirmed by the elementary mapping of calcium, phosphorous, and titanium. X-ray diffraction pattern showed that crystalline HA was present in the HA coating. Microscopic images after actin staining with rhodamine phalloidin revealed that the spread of clonal stromal cells was markedly greater on HA coating than on untreated TW. When infused with clonal stromal cells, the HA-coated TW could indeed generate bone formation in the backs of nude mice. However, the appearance of new bone was not enhanced by the HA coating, likely because air in the porous scaffold during cell loading reduces the cell-scaffold contact. Mild vacuum loading techniques might enable differences of osteo-differentiation between HA-coated TW and non-coated TW to emerge.