Anisotropic pore structure affects fluid storage and transport behaviors in rock matrix. In this study, we quantitatively investigate the anisotropic pore structure properties of coal and shale through small-angle neutron scattering associated with contrast-matching method. Experimental 2D scattering profiles from the samples cut parallel and perpendicular to the bedding indicate isotropic 3D spherical scattering profile for Hazleton coal and anisotropic 3D ellipsoidal scattering profile for Marcellus shale. Apparent porosity and surface area of total pores are similar between the samples cut parallel and perpendicular to the bedding for Hazleton coal but are higher for the sample cut perpendicular to the bedding than the sample cut parallel to the bedding for Marcellus shale. Apparent pore accessibility follows the trend powder sample > sample cut perpendicular to the bedding > sample cut parallel to the bedding for both the measured coal and shale, indicating nanopores near the surface of granular particles have higher pore accessibility than those inside granular particles. It was captured that the measured coal has less porosity, surface area, and pore accessibility than the measured shale for each type of sample. In addition, based on the apparent pore properties of accessible pores, microscopic transport mechanism could be that fluid preferably diffuses along the bedding direction in coalbed methane and shale gas reservoirs.