The complexity of the pore structure, spatial development, fractures, and pore distribution of fractured-vuggy carbonate reservoirs influences the water invasion dynamics of gas reservoirs, which is crucial in the dynamic research of strongly heterogeneous reservoirs. In this study, the collocation relationship of pore-vuggy fractures is described by the quantitative characterization of their attribute parameters. The discrete fracture network model is used to match and construct the fractures in different modes. The distribution classification method is used to model three-dimensional geological reservoirs in terms of their geometric and attribute characteristics. Bottom-water and edge-water gas reservoirs are constructed separately using numerical simulation, and the dynamic characteristics of water invasion are described. The results show that the proposed method is suitable for the geological modeling of fractured-vuggy gas reservoirs with strong heterogeneity and complexity. The modeling accuracy is improved because the gas reservoir heterogeneity and water invasion’s dynamic characteristics can be described accurately. Six stages of water invasion are identified from the numerical simulation of water invasion. This method provides theoretical guidance for the study of heterogeneous gas reservoirs with water.