The KT-II reservoir in the B oilfield is a structurally lithological composite layered carbonate reservoir with gas cap and edge bottom water. In 2021, black oil was produced from wells that were previously identified as gas layer, Indicating that the accuracy of the original understanding of the oil and gas interface is no longer sufficient to meet the current development requirements. In response to the complex distribution of the reservoir storage and the lack of implementation of the original oil and gas interface, referring to the concept of individua sand bodies in clastic rocks, a definition of carbonate reservoir storage unit is proposed. Then, through three-dimensional geological modeling, fine characterization of carbonate reservoir storage units is carried out, and based on this, numerical simulation research is conducted. By conducting a detailed study on the individual reservoirs in the reservoir, the spatial distribution patterns between the storage units and non reservoirs were described in detail. Different oil and gas interfaces were established in different regions to accurately describe the distribution of oil, gas, and water in carbonate reservoirs. The contradiction of producing black oil in the “gas layer” of the production well was reasonably explained, and the correctness of the model was verified through upward return well production later. This method improves the accuracy of research on the distribution of oil, gas, and water in carbonate reservoirs, and has guiding significance for the study of the relationship between oil, gas, and water in complex layered carbonate reservoirs and the exploration of remaining oil potential.