As the commercial development of shallow shale gas reservoirs has been successfully achieved in Sichuan Basin, the deep shale gas reservoirs become the key development target in the next step. The accurate quantitative characterization of the fluid storage and structural properties of deep shale is of great significance in resource evaluation and gas exploitation. In this study, fifteen deep Longmaxi Formation shale samples belonging to three sublayers are collected from the L208 well area, Luzhou Block, southern Sichuan Basin. Nuclear magnetic resonance and nitrogen adsorption are conducted on these samples to obtain the fluid storage capacity and microstructural information. Pore fractal dimension and surface fractal dimension are interpreted from these experimental data for quantitative evaluation of the pore distribution complexity and pore surface irregularity, respectively. The controlling factors of storage and microstructural properties of these deep shales are analyzed. From the perspective of stratigraphic division, the shales belonging to the lower sublayers possess a larger transverse relaxation time of the main peak, a weaker nitrogen adsorption amount, a lower pore volume, a lower specific surface area, and a higher surface fractal dimension as compared to those of the shales from the upper sublayer. From the perspective of shale composition, clay mineral content and total organic carbon content are the main and minor controlling factors of the storage capacity, pore fractal dimension, and surface fractal dimension of deep Longmaxi shale, respectively. Moreover, the pore surface irregularity is relevant to the average pore diameter and specific surface area.