In the reconstruction of bone defects close to soft tissue, preventing the invasion of fibrous tissue into the bone defect is key to successful bone reconstruction. In this study, we clarified the effects of the pore architecture of artificial bone grafts on the penetration of bone and fibrous tissue, and the orientation of regenerated bone. Carbonate apatite grafts with uniaxial pores along the long- (L-graft) or short-axis (S-graft) direction of the graft and biaxial pores along the long- and short-axes (LS-graft) were used. These grafts were implanted in bone defects created by rabbit ulnae amputation. The pores of the L-, S-, and LS-grafts opened into the bone stumps, muscles, and bone stumps and muscles together, respectively. In the L-graft, the graft pores developed bone from the bone stump to the graft center, while preventing excessive invasion of fibrous tissue. In S- and LS-grafts, the graft pores along the short axis allowed the invasion of fibrous tissue into the grafts. Consequently, although the bone grew to the edge regions in these grafts, further bone ingrowth was inhibited by the fibrous tissue. Furthermore, the pore architecture of the grafts affected the orientation of the regenerated bone. The degree of orientation of the bone formed in the L- and S-grafts was 1.6-fold higher than that formed in the LS-grafts. Thus, controlling the pore architecture allowed the growth of bone to predominate over that of fibrous tissue and induced the formation of bone with an ordered orientation