Carbonate reservoirs are rich in oil and gas reserves; thus, they have great exploitation potential. Therefore research on the microscopic mechanisms of carbonate reservoirs is of great significance. Based on the thin section images of core castings of typical Well 555 and its pore and fracture features in actual reservoirs, this study designed three kinds of images representing the pore and throat structure of real rocks by applying image stitching and binarization processing methods. A microscopic pore model of carbonate rocks was then established using COMSOL numerical simulation software. The microscopic water flooding characteristics and residual oil distributions of different schemes were observed by designing different fracture development forms. The fractures that developed in parallel main lines showed a more obvious influence on water flooding characteristics compared to fractures that developed in vertical main lines. The cluster residual oil was the main residual oil type in the early stage of water flooding in the pure matrix model. With the progress of water flooding, the continuous cluster residual oil gradually turned into mainly discontinuous porous and columnar residual oils. Vertical mainline fractures reduced the amount of residual oil in clusters and replaced it with columnar residual oil. In contrast, parallel main line fractures expanded the unswept area, with the residual oil appearing in contiguous clusters. This study microscopically analyzed the law and characteristics of water flooding in carbonate reservoirs to provide key theoretical support for enhancing oil recovery.