Multiscale pore structures of shale conjunctionally determine the gas storage and transport properties of gas shale reservoirs. To investigate the complex pore structures and gas transport in the ultra-tight porous media, a combination of petrophysical and scanning measurements is adopted in this study. Five shale samples of the main productive layers from four wells (Long 1(1) sub-members of Longmaxi Formation) in southeast Sichuan Basin, China are analyzed. Based on scanning electron microscope (SEM) image, different types of organic pores and inorganic pores are quantitatively analyzed. A method for identification of organic and inorganic pores from SEM images is developed. And a comparison between the pores identified from SEM and gas adsorption (N-2 and CO2 adsorption) is conducted. Results show that the main part of inorganic pores are mesopores, and the organic pore size distributions tend to be lognormal with the peak pore size from 10 nm to 30 nm. Results also show that the gas storage space obtained by SEM is several times to several tens of times larger than that obtained by gas adsorption method. The permeability of OM and shale cores is also compared. The permeability is strongly anisotropic and all those samples show a significant non-Darcy effect. Finally, the relationship between the pore structures and gas transport behavior is studied, and the high quality shale samples are identified considering their gas storage and transport behaviors.