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Carbonate reservoirs exhibit strong heterogeneity in the distribution of pore types that can be quantitatively characterized by applying Xu–Payne multi-porosity model. However, there are some prerequisites to this model the porosity and saturation need to be provided. In general, these application conditions are difficult to satisfy for seismic data. In order to overcome this problem, we present a two-step method to estimate the porosity and saturation and pore type of carbonate reservoirs from seismic data. In step one, the pore space of the carbonate reservoir is equivalent to a single-porosity system with an effective pore aspect ratio; then, a 3D rock-physics template (RPT) is established through the Gassmann’s equations and effective medium models; and then, the effective aspect ratio of pore, porosity and fluid saturation are simultaneously estimated from the seismic data based on 3D RPT. In step two, the pore space of the carbonate reservoir is equivalent to a triple-porosity system. Combined with the inverted porosity and saturation in the first step, the porosities of three pore types can be inverted from the seismic elastic properties. The application results indicate that our method can obtain accurate physical properties consistent with logging data and ensure the reliability of characterization of pore type.