The Xiagou Formation is the main tight oil reservoir in Qingxi Sag of Jiuquan Basin. Given the poor physical properties and other factors restricting tight oil exploitation and production in this area, studies should focus on microscopic pore structure characteristics. In this study, a nano-CT scanner, a SEM, and an NMR were used to study the pore structure characteristics of a tight carbonate reservoir in Qingxi Sag, Jiuquan Basin. The Xiagou Formation reservoir mainly consists of gray argillaceous dolomite and dolomitic mudstone. The pore categories are mainly elliptic, irregular, intergranular, and intragranular and mostly filled with clay and carbonate cement. Pore space is small, the intergranular or organic pores are mostly separated, and pore-throat is weakly connected. The throats mostly develop with lamellar and tube bundle-like characteristics and with poor seepage ability. The pore-throats mostly span from nanometer to micrometer sizes, and pore diameters are mainly concentrated in the range of 0.01–0.1 and 1–10 μm. It is a unimodal pattern mainly composed of micropores, or a bimodal regular allocation dominated by micropores supplemented by macropores. The relationship between micropore (<0.1 μm) and macropore (>1 μm) content allocation and mean pore diameter strongly controls the permeability of reservoir rocks. When macropore content reaches more than 85%, or when pore content totals less than 3%, the permeability of a reservoir remarkably increases. At a higher ratio of the average finest throat sectional area and throat-pore of reservoir rock, the throat radius lies closer to the connecting pore radius, pore and throat connectivity improves, and reservoir seepage ability becomes stronger. Based on reservoir capacity and seepage ability, pore structures of the tight carbonate reservoirs in study area are classified into type I (small-pore–thin-throat), type II (thin-pore–thin-throat), and type III (microporous-microthroat) with rock permeability>0.1 mD, 0.05–0.1 mD, and <0.05 mD, respectively. The type I pore structure reservoir should be regarded as an indicator of tight oil “sweet spots” reservoir in the study area.