Abstract: The utilization of low-salinity waterflooding (LSW) as a promising enhanced oil recovery method has exhibited exciting results in various experiments conducted at different scales. For carbonate rock, pore-scale understanding of the fluid distribution and remaining oil after LSW is essential, especially the geometry and topology analysis of oil clusters. We performed the tertiary LSW and X-ray micro-CT was utilized to probe the pore-scale displacement mechanism, fluid configuration, oil recovery, and remaining oil distribution. We found that the core becomes less oil-wet after LSW. Furthermore, we analyzed the oil–rock and oil–brine interfacial areas to further support the wettability alteration. By comparing images after high-salinity waterflooding (HSW) and LSW, it is proven that wettability alteration has a significant impact on the behavior of the two-phase flow. Our research demonstrates that LSW is an effective tertiary enhanced oil recovery technology in carbonate, which changes the wettability of rock and results in less film and singlet oil.