The control of the morphology and polymorphs of CaCO3 has been required, since their capabilities are dependent on particle characteristics of CaCO3. It is difficult to clarify the formation mechanism only by the experimental approaches because the nucleation and crystal growth of CaCO3 occurred at nanoscale. The objective of the present work is to investigate the effect of surface properties including in the charge density and the dielectric constant of water on the aggregation process of primary particles by means of molecular dynamics simulations. The grain boundary energy was also calculated by molecular dynamics simulation to investigate the change of energy in the aggregation process of primary particles. From the results of molecular dynamics simulation, we found that the interface of (001)Ca and (001)CO3 contacted with water charged positively and negatively and the interface of (100) and (104) contacted with water charged neutrally. When the distance of interfaces between CaCO3 particles came close to colliding, the dielectric constant of water became small except the interface of (001)CO3. The boundary energy of interface between (001)Ca and (001)CO3 was the lowest among five types of interfaces. It indicates that the aggregation of (001)Ca and (001)CO surface is the easiest among all types of interfaces.