Carbonate reservoirs are characterized by abundant reserves and are currently focal points for development in oil and gas producing regions such as the Ahdab oilfield, Tarim Basin, Sichuan Basin, and Ordos Basin. The primary method for exploiting carbonate reservoirs is waterflooding. However, due to the complex pore structure and pronounced heterogeneity of carbonate rocks, the waterflooding process often leads to an unclear distribution of remaining oil and low waterflooding recovery efficiency, significantly impacting the stable and high production of carbonate reservoirs. This paper presents a two-phase flow model of oil and water in distinct pore structures by integrating fluid flow equations and interface tracking equations. It visually represents the waterflooding process at the pore scale, elucidates the distribution and formation mechanism of remaining oil, and discusses the mechanism of microscopic displacement efficiency change. The study reveals that: 1) After waterflooding, the distribution patterns of remaining oil can be categorized into dead-end remaining oil, pressure balance remaining oil, wall-bound remaining oil, Jamin effect remaining oil, and water-encapsulating remaining oil, which are governed by microscopic pore structure, wettability, and preferential flow paths; 2) From the perspective of actual reservoir displacement efficiency, intergranular pores > intergranular dissolved pores > visceral foramen > mould pore, with this trend being more pronounced under hydrophilic wetting conditions; 3) Given the oil-wet to strong oil-wet wettability characteristics of these carbonate rocks, capillary forces pose significant resistance during waterflooding. The conclusion underscores the importance of leveraging the reservoir’s microscopic pore structure and wettability characteristics for actual oil wells, elucidating the evolutionary law of the mechanical mechanism of oil-water interface advancement, clarifying oil-water percolation characteristics at the pore scale, and understanding the microscopic displacement physical mechanism, all of which are crucial for guiding the design of schemes aimed at enhancing reservoir recovery efficiency.