In a shale gas reservoir, pore characterization is an important factor used to determine gas storage capacity. However, the nanometer (nm)-scale pore system in shale is difficult to explore by traditional optical, scanning electron microscopy, or even nuclear magnetic resonance well logging. We have investigated the pore structure and storage capacity of the Marcellus Shale through integration of petrophysical analysis from laboratory 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 the 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 properly used to approximate the shale porosity and estimate the shale gas volume. In addition, the specific surface area, micropore, and mesopore volumes have a positive relationship with the kerogen volume and total organic content (TOC). By using the Langmuir and Brunauer-Emmet-Teller models, the simulated result indicates that the higher adsorbed quantity of the Marcellus Shale could be the result of the increase of micropore volume contributed, by the increase of kerogen or TOC content. The proposed equations rapidly compute TOC, a key parameter to predict gas storage capacity in overmature shale such as the Marcellus Shale.