The low-permeability conglomerate reservoir in the Mahu Sag has great resource potential, but its strong heterogeneity and complex microscopic pore structure lead to a high oil-gas decline ratio and low recovery ratio. Clarifying the migration rule of crude oil in microscopic pore throat of different scales is the premise of efficient reservoir development. The low-permeability conglomerate reservoir of the Baikouquan Formation in the Mahu Sag is selected as the research object, and two NMR experimental methods of centrifugal displacement and imbibition replacement are designed to reveal the differences in the migration rule of crude oil in different pore throats. According to the lithology and physical properties, the reservoirs in the study area can be divided into four categories: sandy grain-supported conglomerates, gravelly coarse sandstones, sandy-gravelly matrix-supported conglomerates and argillaceous-supported conglomerates. From type I to type IV, the shale content of the reservoir increases, and the physical property parameters worsen. Centrifugal displacement mainly produces crude oil in large pore throats, while imbibition replacement mainly produces crude oil in small pores. In the process of centrifugal displacement, for type I reservoirs, the crude oil in the pore throats with radii greater than 0.5 μm is mainly displaced, and for the other three types, it is greater than 0.1 μm. The crude oil in the pore throats with radii of 0.02–0.1 μm, which is the main storage space for the remaining oil, is difficult to effectively displace. The crude oil in the pore throats with radii less than 0.02 μm cannot be displaced. The two experimental methods of centrifugation and imbibition correspond to the two development methods of displacement and soaking in field development, respectively. The combination of displacement and soaking can effectively use crude oil in the full-scale pore throat space to greatly improve the recovery of low-permeability conglomerate reservoirs.