Hydroxyapatite (HA) plays an important role in clinical bone repair. However, it remains a challenge to accurately determine its changes during bone reconstruction and to identify its differences from native bone apatite. Here, terbium (Tb) doped uniform HA nanocrystals were implanted into bone tissue and compared with native bone apatite. These comparisons demonstrated the occurrence of compositional and structural alteration of the implanted HA nanocrystals, and their gradual degradation, during bone reconstruction. They also revealed notable differences between HA nanocrystals and bone apatite crystals in crystal size, distribution pattern, and state of existence in bone tissue. Although synthetic HA nanocrystals could osteointegrate with bone tissue, they still seemed to be treated as foreign material in this tissue and thus were gradually degraded. These findings can help to identify and rethink the function of synthetic apatite and bone apatite, which will benefit future design and application of biomimetic bone repair materials.