Pore structure in shale is an important factor influencing the storage capacity of a shale gas reservoir and the effect of shale gas development. Taking the core and outcrop shale samples from the Lower Cambrian Niutitang Formation and Lower Silurian Longmaxi Formation as the object of the research, combined with the scanning electron microscope, high pressure mercury injection, CO2 and N2 gas adsorption experiments, we investigated the porosity, pore types, pore structure, and pore size distribution of the Lower Paleozoic shale gas reservoirs in northern Guizhou, South China. The results indicated that there are developed various genetic types of micro-nano pores in the Lower Paleozoic marine shale in northern Guizhou, which provide the main reservoir spaces for shale gas. The porosity of the Lower Paleozoic shale in northern Guizhou is 1.30%–13.37% in range, and the average is 4.56%. The inter-granular pore, organic matter pore and intra-granular pore are most common. Micropore (<2 nm) and mesopore (2–50 nm) are the main reservoir storage space for shale gas. The specific surface area of micropore plus mesopore in the Lower Paleozoic shale accounts for 94.3% of the total specific surface area, and their pore volume accounts for 59.1% of the total pore volume in northern Guizhou. The pore size of the Lower Paleozoic shale is mainly distributed in 0.4–0.7 nm, 3–10 nm and 0.05–200 μm. The pore structure is the parallel-plate pore with slit shape, two-ends-opened tube pore and ink-bottle shape pore. There are significant differences in the porosity and pore size between the Longmaxi Formation shale and the Niutitang Formation shale. The average porosity and average pore size of the Longmaxi Formation shale is 6.4% and 4.71 nm, while the Niutitang Formation shale is 5.3% and 4.23 nm, respectively. The pore structure of the Lower Paleozoic shale gas reservoir is mainly influenced by organic matter abundance, thermal maturity, mineral composition of shale. The porosity and micropore volume of shale show an increasing trend, with the increase of total organic carbon content and quartz content. The porosity and pore volume of shale have a decreasing trend, with the increase of thermal maturity level and clay mineral content.