In a shale gas reservoir, pore characterization is an important factor to determine gas storage capacity. However, the nanometer (nm) scale pore system in shale is difficult to explore by traditional optical, scanning electron microscopy (SEM) or even nuclear magnetic resonance (NMR) well logging. We investigated the pore structure and storage capacity of the Marcellus Shale through integration of petrophysical analysis from lab and well logging data, and nitrogen adsorption. The isotherm of Marcellus Shale is a composite isotherm, which has features of Type I, Type II and Type IV isotherms with Type H4 of hysteresis loop, suggesting slit-like pores developed in the Marcellus Shale. Quantitative analysis of pore volumes from the nitrogen adsorption indicates that density porosity may be more proper to approximate shale porosity and estimating the shale gas volume. In addition, the specific surface area, micropore and mesopore volumes have positive relationship with kerogen volume and total organic content (TOC). By employing Langmuir and Brunauer-Emmet-Teller (BET) models, simulated result indicates that higher adsorbed quantity of the Marcellus Shale could be the result of increase of micropore volume contributed, by increase of kerogen or TOC content. The proposed equations rapidly compute TOC, a key parameter to predict gas storage capacity in over-matured shale such as the Marcellus Shale.