The invention discloses a modeling method used for representing the gas-water distribution of water-borne carbonate rock gas reservoir and relates to a six-stage modeling method. Based on the characteristics of a water-borne carbonate rock gas reservoir of the development of pores, cavities and crevices, the complex spatial combination types of the pores, cavities and crevices, the coexistence of layered edge water and uneven bottom water, the complex gas-water relations, etc., the invention proposes the six-stage modeling method of stratigraphic bedding plane structure modeling, sedimentary facies modeling, reservoir permeability medium facies modeling, gas-water interface modeling, fluid classification facies modeling and porosity, permeability and gas saturation property modeling, and the accurate quantitative representation of the gas-water distribution of water-borne carbonate rock gas reservoir in a three-dimensional space is realized. Compared with the water-borne carbonate rock gas reservoir model established by means of the conventional three-stage modeling method, the three-dimensional quantitative geological model of the gas-water distribution of water-borne carbonate rock gas reservoir is more accurate and reliable and can be widely used in each stage of the exploitation of water-borne carbonate rock gas reservoirs.