This paper quantitatively evaluates the hierarchical structure of multiple-porosity systems, including natural micro-fractures, inter-granular, and intra-granular pores, using nuclear magnetic resonance (NMR) measurements. Conventional well logs cannot distinguish between different pore structures. NMR measurements, although counted among the most reliable methods to measure formation porosity, has been conventionally considered as insensitive to the existence of natural fractures. Thus, the impact of natural micro-fractures on NMR measurement has rarely been investigated.We simulated NMR response in porous media using a random-walk algorithm. We randomly distributed and oriented natural micro-fractures in various porous rock matrices. We then quantified the sensitivity of NMR T 2 (spin-spin relaxation time) distribution to the presence of natural fractures within (a) three-dimensional (3D) Micro-Computed Tomography (micro-CT) images of carbonate and sandstone rock samples and (b) synthetic organic shale matrices.Results from synthetic rock samples showed that NMR T 2 distribution can be significantly affected by aperture, concentration, and shape (e.g., needle-like or planar shape) of natural fractures, as well as size and connectivity of inter-granular pores. We also quantified the impact of diffusional coupling effect between the micro-fractures and inter-granular pores on NMR T 2 distribution. Applications of this research include reliable reservoir characterization in challenging multiple-porosity systems such as naturally fractured carbonates and organic-rich source rocks, where (a) conventional well logs cannot reliably characterize the complex pore structure and (b) interpretation techniques for unconventional logs such as NMR are not fully developed.