The property changes of low-permeability oil reservoirs after long-term water flooding remain insufficiently understood. This study conducted water flooding experiments on three real core samples and employed scanning electron microscopy (SEM), X-ray diffraction (XRD), and nuclear magnetic resonance (NMR) to analyze how the changes in mineral and pore structure relate to permeability changes before and after water flooding. The results showed that the core permeability decreased significantly after water flooding, with a decrease rate of 69.7%, 19.6%, and 34.4% for the three cores. The well test results of the block also indicate that the reservoir permeability decreases after long-term water injection, with an average decrease of over 60%. The clay mineral content decreased notably, with the largest decrease of 8.6 percentage points in kaolinite and minor decreases in chlorite and illite. SEM results also indicated erosion and damage to the clay mineral structure by the water flow, and kaolinite has a high degree of dissolution. The NMR results showed that after water flooding, the pore size curve shifted to the left, the relaxation time decreased, the number of small pores in the cores increased, and the number of large pores decreased. The median pore radius decreased by 3.4% to 21.53%.