In order to carry out research on variation of microheterogeneity in sandstone reservoir after long-term water flooding in the complex faulted oilfields, the cores are cut from typical wells of main oil layers of two blocks in the Jidong Oilfield, and the experiments of long-term water flooding are conducted. Based on the mercury-injection data at different water cut stages during water flooding and the digital core data reconstructed by X-ray CT scanning, the variation of microheterogeneity of reservoir at different water cut stages during long-term water flooding of core are quantitatively characterized through fractal dimension method and 3D pore network model, and the rule of oil-water seepage at different water cut stages is characterized. The study showed that the middle-high-permeability reservoir has a good fractal structure with fractal dimension between 2 and 3. The large pore has the less fractal dimension, and the better homogeneity and pore structure than the small one. After the cores are washed by long-term water flooding, and as the water cut increases, the fractal dimensions of large and small pore gradually decrease, mean and medium pore diameters increase, the relative sorting coefficient decreases, the distribution probability of throat radius of core generally increases, and the microheterogeneity of reservoir weakens. Moreover, the oil relative permeability curves are almost overlapped, and the water relative permeability curves result in a big difference. Under the same water saturation, as the water cut increases, the fractal dimension decreases, the water relative permeability increases, and the oil-water common seepage points shift to the left.