Molecular dynamics (MD) simulation was used to study chitosan behaviors on different hydroxyapatite (HA) crystallographic planes at the atomic level. The interaction energy between the chitosan chain and different HA surfaces indicates that the interaction of the chitosan chain and HA(1 0 0) surfaces is stronger than that of HA(0 0 1) and HA(1 1 0) surfaces. The chemical interactions between chitosan and HA were analyzed through the concentration profile and pair correlation function of nitrogen and oxygen atoms in chitosan. The results show that there might be chemical interaction between nitrogen and calcium atoms, and hydrogen bonding between oxygen atoms and hydroxyl groups. This study provides useful information in understanding the interfacial interaction mechanism at the atomistic scale.