An investigation into microscopic pore structures and their primary controlling factors was conducted on a paralic shale reservoir on the Upper Paleozoic in Erdos Basin, using field-emission scanning electron microscopy, high-pressure mercury intrusion, and low-temperature nitrogen adsorption. Pore morphology and pore size distributions from macropores to micropores were successfully characterized. Combined with geochemical parameters and mineral compositions, the factors influencing nanoscale pore structures were analyzed. The results indicate that the pores in the shale reservoirs are generally nanoscopic, and can be classified into four types, namely, organic pores, intergranular pores, intraparticle pores and micro-fractures, of which the most common are organic nanopores and interparticle pores between clay particles. The results of high-pressure mercury intrusion and low-temperature nitrogen adsorption show that the majority of pores consist of micropores and transitional pores, and that pore size distributions are multimodal, including the ink-bottle and parallel plate types. Micropores and transitional pores account for most of the pore volume, whereas the specific surface area is attributed to the micropores. Furthermore, the organic carbon content (TOC) and clay mineral content are primary factors in determining the nanoscale pore structure characteristics, of which the TOC controls the development of micropores and the structure of transitional pores. Clay mineral has an effect on micropores, and the brittle mineral benefits both micropores and macropores.