Herein, the interfacial effects on calcium carbonate clustering within two-dimensional (2D) graphene nanochannels were systematically investigated using molecular dynamics simulations. The distribution characteristics of the ions at the interface can be attributed to the ordered water layers within the 2D nanochannels. The orientation of CO32- is approximately perpendicular to the interface, which can be attributed to hydrogen bonding and its association with Ca2+ at the interface region. The results show that characteristics of CaCO3 clusters can be affected by ion dynamics at the interface and nanoconfinement, although they prefer to locate in the bulk-like region. Due to nanoconfinement, ion dynamics are slowed down, especially in the direction perpendicular to the graphene surface. Due to the distribution and orientation characteristics of CO32- in the interface region, particularly considering the hydration dynamics of Ca2+ and CO32-, the association between Ca2+ and CO32- ions in CaCO3 clusters at the interface can be promoted as Ca2+ moves from the interface region to the bulk-like region. The ion dynamics and coordination characteristics of CaCO3 near the interface region within 2D nanochannels facilitate the formation of CaCO3 clusters with highly coordinated Ca2+-CO32- structures, which might favor the nucleation of aragonite. The results provide insight into the effects of nanoconfinement and interfacial water layers on biomineral nucleation and offer theoretical insights into the new preparation methods of novel inorganic functional materials.