Changes in the biological apatite (BAp) c-axis orientation were investigated as a bone quality parameter in bone regeneration using hydroxyapatite/poly ɛ-caprolactone (HA/PCL) composite scaffolds. Three-dimensional (3D) HA/PCL composite scaffolds were fabricated using a layer manufacturing process in three grid sizes (200-, 600-, and 1000 μm) and grafted into the forearm ulna of New Zealand white rabbits. The cross-sectional areas of the bones regenerated from the scaffolds with 600- and 1000-μm grid sizes were significantly larger than those from the scaffold with 200-μm grid sizes, whereas bone mineral density in the regenerated regions did not differ between the three grid sizes. Moreover, the BAp c-axis orientation in the bones regenerated from the scaffolds with grid sizes of 600- and 1000 μm was not significantly different; however, both scaffolds showed enhanced BAp orientation, although the degree of BAp orientation was lower than that in intact bones. In conclusion, HA/PCL composite 3D scaffolds with 600- and 1000-μm grid sizes induced BAp c-axis orientation and showed good bone regeneration behavior in vivo.