Abstract: The pore structure of ultra-low permeability sandstone is highly complex, with strongly heterogeneous wettability, which complicates the characterization of oil–water flow behavior and remaining oil distribution during waterflooding. Current research methods mainly rely on core-scale experimental analysis, which falls short in accurately capturing pore-scale dynamic flow processes in heterogeneous porous media. As a result, the microscopic mechanisms of oil displacement remain inadequately understood. To address this, visual models based on real core samples from ultra-low permeability reservoirs in the Ordos Basin were constructed to conduct waterflooding experiments. Numerical simulations were also employed to investigate the characteristics of oil–water flow and distribution during waterflooding. The results demonstrate that waterflooding in ultra-low permeability rocks follows a fingering displacement pattern. Both a reduction in pore-throat radius and an increase in heterogeneity lead to decreased oil displacement efficiency. Increasing the injection rate improves oil displacement efficiency in oil-wet rocks by up to 17%, whereas in water-wet rocks, it first increases and then decreases, peaking when viscous and capillary forces reach equilibrium. As rock wettability shifts from strongly water-wet to strongly oil-wet, oil displacement efficiency decreases by 20.2%, and the dominant forms of remaining oil transition from corner and throat types to clustered and interconnected types. Under mixed-wettability conditions, water phase flow paths alter significantly, with the proportion of clustered remaining oil being 17.2%–33.4% higher compared to purely oil-wet or water-wet systems. This leads to lower sweep efficiency and displacement efficiency relative to homogeneous wettability systems. Due to capillary effects, the wettability at the pore inlet plays a decisive role in controlling fluid flow under mixed-wettability conditions. This study provides an important theoretical foundation for the effective development of water injection in ultra-low permeability reservoirs.