Pore type variations account for complex velocity-porosity relationship and intensive permeability heterogeneity and consequently low oil and gas recovery in carbonate reservoir. However, it is a challenge for geologist and geophysicist to quantitatively estimate the influences of pore type complexity on velocity variation at a given porosity and porosity-permeability relationship. A new rock physics-based integrated approach in this study was proposed to quantitatively characterize the diversity of pore types and its influences on wave propagation in carbonate reservoir. Based on above knowledge, permeability prediction accuracy from petrophysical data can be improved compared to conventional approach. Two carbonate reservoirs with different reservoir features, one is a shallow carbonate reservoir with average high porosity (>10%) and another one is a supper-deep carbonate reservoir with average low porosity (<5%), are used to test the proposed approach. Paleokarst is a major event to complicate carbonate reservoir pore structure. Because of limited data and lack of appropriate study methods, it is a difficulty to characterize subsurface paleokarst 3D distribution and estimate its influences on reservoir heterogeneity. A method by integrated seismic characterization is applied to delineate a complex subsurface paleokarst system in the Upper San Andres Formation, Permian basin, West Texas. Meanwhile, the complex paleokarst system is explained by using a carbonate platform hydrological model, similar to modern marine hydrological environments within carbonate islands. How to evaluate carbonate reservoir permeability heterogeneity from 3D seismic data has been a dream for reservoir geoscientists, which is a key factor to optimize reservoir development strategy and enhance reservoir recovery. A two-step seismic inversions approach by integrating angle-stack seismic data and rock physics model is proposed to characterize pore-types complexity and further to identify the relative high permeability gas-bearing zones in low porosity reservoir (< 5%) using ChangXing super-deep carbonate reservoir as an example. Compared to the conventional permeability calculation method by best-fit function between porosity and permeability, the results in this study demonstrate that gas zones and non-gas zones in low porosity reservoir can be differentiated by using above integrated permeability characterization method.