Water flooding is one of the important methods for developing ultralow permeability reservoirs. However, due to the high clay mineral content in these reservoirs and poor compatibility between injected water and formation fluids (such as formation water), the reservoirs suffer damage. Previous studies have lacked research on the dynamic damage patterns of internal structures during the water flooding process in ultralow permeability cores. Addressing this, this study focuses on an ultralow permeability reservoir in northwest China, analyzing the pore-permeability characteristics, pore structures, and clay mineral composition of core samples. Using core nuclear magnetic resonance displacement technology, it examines microstructural changes in pore spaces at various locations and employs microfluidic experimental techniques to replicate the transport behavior of scale particles during water flooding in low permeability porous media. Together, these findings reveal the damage mechanisms of this ultralow permeability reservoir, where free particles migrate with injected water to clog the rear part of the reservoir, significantly reducing the reach of the water flood. Therefore, for the water injection development of low-permeability oil reservoirs, attention should be paid to improving the quality of the injected water. Functional chemicals such as scale inhibitors and clay stabilizers should be added to the injected water in advance, and reservoir modification operations such as acidizing and fracturing should be carried out promptly. This minimizes the damage of these free particles to the deep reservoir and increases the sweep efficiency of water flooding.