Chang 6 3 reservoir in Huaqing oilfield, Ordos Basin, China is featured by strong pore structure heterogeneity, which leads to prominent Jamin effect in the water flooding, difficult development process, low productivity, and massive residual oil. Accordingly, this study aims to explore the microscopic pore structure of Chang 6 3 reservoir and investigate its influence on the water flooding efficiency, based on a series of comprehensive analyses, including physical property analysis, casting thin section observation, scanning electron microscopy measurement, high-pressure mercury injection, constant rate mercury injection, and microscopic real sandstone water flooding model. It is demonstrated that gray and gray-brown feldspathic sandstone are the main reservoir lithology in the study area, with dominant pore types of residual intergranular pores and feldspar dissolution pores. Pore throat radius is unevenly distributed, and small and micro pores take the majority. Based on the comparison of capillary pressure curve characteristics and comprehensive analysis of corresponding parameters, the pore structure of the Chang 6 3 reservoir is divided into four types, namely types I-IV. They have different reservoir spaces, and their reservoir and seepage capacities decrease in the order of types I-IV pore structures. Moreover, displacement patterns in them are also different, with the finger-like-reticular displacement as the primary. In addition, pore throat radius and distribution play a critical role in the water flooding. It is also demonstrated that the water flooding efficiency increases with permeability and porosity, pore structure quality, and pore throat distribution evenness.