The utilization of low-salinity waterflooding 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 low-salinity waterflooding is essential, especially the geometry and topology analysis of oil clusters. We performed the tertiary low-salinity waterflooding and employed X-ray micro-CT 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 low-salinity waterflooding. Furthermore, we analyzed the oil-rock and oil-brine interfacial areas to further support the wettability alteration. By comparing images after high-salinity waterflooding and low-salinity waterflooding, it is proven that wettability alteration has a significant impact on the behavior of the two-phase flow. Our research demonstrates that low-salinity waterflooding is an effective tertiary enhanced oil recovery technology in carbonate, which changes the wettability of rock and results in less film and singlet oil.