<p>In recent decades, with the advancement of detection technologies, the exploration and development of deep carbonate reservoirs worldwide have progressed continuously, the number of oil and gas reservoirs has continued to increase. Compared with sandstone reservoirs, the enrichment patterns of carbonate reservoirs are substantially more complex. In recent years, petroleum geologists have deepened their understanding of capillary pressure due to the continuous expansion of reservoir formation research, supplemented by new methods and techniques. Numerous scholars have begun to focus on the positive impact of capillary pressure on hydrocarbon migration and accumulation. Determining the variation in capillary pressure in carbonate rocks with burial depth is of considerable importance for understanding the mechanisms of oil and gas enrichment. In this study, molecular dynamics simulations were used to determine the relationship between oil–water interfacial tension and depth variation in carbonate reservoirs. The data obtained from previous experiments were then used to obtain changes in contact angle and pore-throat radius with depth. Finally, a new model for capillary pressure variations with depth in carbonate reservoirs is derived based on interface tension, contact angle, and pore-throat radius. The results indicate that the interfacial tension of carbonate rocks decreases with increasing burial depth. The contact angle decreases with increasing temperature and increases with increasing pressure. The variation of capillary pressure with burial depth is related to porosity, permeability, and depth. The new model developed in this study is beneficial for understanding the formation mechanisms of carbonate reservoirs, providing guidelines for oil exploration and development in deep or even ultradeep carbonate reservoirs.</p>