Calcium carbonate nanoparticles are often surface-treated with organic compounds such as fatty acids. The activated calcium carbonates not only exhibit excellent application properties, but also can be applied as eco-friendly inorganic-organic hybrid materials. However, the microscopic adsorption structure of organic compounds on calcite surfaces is not yet well understood. In this study, we performed computational simulations based on density functional theory to investigate adsorption states of stearic acid (SA) on a calcite (104) surface. Based on the first-principles ionic relaxation and molecular dynamics simulations for several types of SA−SA and calcite−SA bonding models, a SA bilayer model on the calcite (104) surface is predicted to be a possible stable structure. The proposed structure model is well consistent with the experimentally predicted adsorption mechanism of SA on the calcite (104) surface.