To study the influence mechanism of calcite surface structure on water adsorption, molecular dynamic simulation was firstly employed to investigate the adsorption characteristics of water on various calcite surface structure with different types and scales. Then, the water adsorption characteristics in nano-slit with surface defects were investigated, which was used to decipher the formation mechanism of water blocking. Finally, the dangling bond characteristics and surface energy results were combined to explain the differential adsorption mechanisms. Results showed that calcite surface structure had great influence on water adsorption. Water was preferentially adsorbed and aggregated around the surface structure, and the adsorption strength and density were much higher than those on the ideal calcite surface. Size of surface structure also presented a great influence on water adsorption. The larger the structure, the stronger the water adsorption. Water in the nano-slits rapidly aggregated around the surface structure and formed obvious adsorption protrusions. Then the adsorption protrusions combined into a water film and blocked the flow space. The water blocking effect appeared. The dangling bond density and surface energy of the vacant surface, protrude surface, and ideal surface were 7.275 nm^-2 and 0.734 J/m², 6.716 m^-2 and 0.721 J/m², 5.098 nm^-2 and 0.581 J/m², respectively. There were more active sites with stronger reactivity on the vacant and protrude surface. Therefore, water was preferentially adsorbed on them.