With the rapid progress of imaging methods it is now possible to obtain detailed rock structure information on different scales, ranging from nanometers to micrometers. Such knowledge facilitates use of pore-scale modeling approaches to predict numerous physical properties based on three dimensional structural data. Pore-scale modeling approaches can simulate different processes in the rock under natural conditions (pressure, temperature, etc.), which are more difficult to simulate in the laboratory. This is especially important for unconventional reservoir rocks such as the Bazhen formation siliceous rocks (black shales) used in this study. Based on X-ray microtomography and SEM imaging we develop a detailed categorization of different types of porosities (including micro, i.e. larger than µm size, and nano, i.e. sub-micron size, porosities) for samples of Bazhen siliceous rocks. Standard pore-scale modeling techniques do not account for different flow regimes within different pore sizes. Thus, we develop a pore-network model with different physics of gas flow for micro- and nanoporosity. High-resolution images are used for stochastic reconstructions of 3D structure and subsequently used for modeling of gas permeability. Resulting permeability values are in a good agreement with gas permeabilities measured for Bazhenov siliceous rocks. Finally, we present a framework to model gas permeability of unconventional reservoir rocks using multi-scale 3D structure information based on microCT scans and high resolution SEM/FIB-SEM imaging techniques.