The pore-fracture structure of deep coal reservoirs is highly important for evaluating, exploring, and developing coalbed methane (CBM) resources. This study considers three coal samples from the DJ57 well in the Benxi Formation in the Daning–Jixian block on the eastern margin of the Ordos Basin as the research object. Based on the coal quality parameters of the coal samples, field emission scanning electron microscopy (FE-SEM), gas adsorption experiments, high-pressure mercury intrusion porosimetry (MIP), and microcomputed tomography (micro-CT) scanning were used to quantitatively characterize the nanoscale pores and microscale fractures in deep coal reservoirs and to evaluate the pore-fracture structure at different scales. The results reveal that the pore types in the Benxi Formation coal samples are diverse and include mainly organic matter (OM) pores, inorganic pores (intraparticle and interparticle pores), and microfractures. The organic pores are diverse in shape and mainly exhibit round, oval, and wedge shapes, while the microfractures exhibit slender stripes or serrated curves. The multiscale quantitative characterization of deep coal reservoir pores and fractures is based on a variety of pore characterization methods, and the pore and fracture volume distributions are mainly U-shaped, revealing the coexistence of micropores and microfractures. The volumes of micropores (0.3–2 nm), mesopores (2–50 nm), macropores (50 nm to 10 μm), and microfractures (>10 μm) account for 78.00%, 6.78%, 2.08%, and 13.14%, respectively, of the total pore volume (PV). Based on a full-scale pore-fracture splicing calculation, the total permeability of the Benxi Formation coal samples ranges from 5.77 to 28.22 mD. The observation results indicate that the microfractures are connected to each other, forming a network structure with strong connectivity. The microfractures are mainly associated with pore diameters>100 μm, accounting for approximately 95% of the total permeability. Moreover, micropores in deep coal reservoirs provide a large space for CBM adsorption, and microfractures enhance the seepage capacity of CBM.