This study analyzes the effects of different ions on the wettability of carbonate rock surfaces during low-salinity water flooding, using core flooding experiments, contact angle measurements, and potential tests. The results indicate that reducing the salinity of injection water can effectively improve the recovery of alkaline crude oil. Ion concentration significantly impacts the wettability of carbonate rocks, with Mg2+ and SO42− showing the most substantial effect on contact angle under low salinity conditions, markedly enhancing oil-wet characteristics. Although Ca2+ does not regulate wettability as effectively as the combination of Mg2+ and SO42−, it still promotes contact angle adjustment to some extent, particularly exhibiting notable wettability modulation at specific concentrations. Na+, by contrast, has the weakest effect on wettability. Changes in ion concentrations result in variations in the surface potential of carbonate rocks, which, in turn, influence the adsorption strength of alkaline components, thereby modulating wettability. Under low-salinity water flooding conditions, Mg2+ and Ca2+ can increase surface potential, enhancing the adsorption of oil-phase components, while SO42− promotes the transition of the rock surface toward a more water-wet state by reducing potential. The study concludes that, in terms of enhancing the wettability of carbonate rock surfaces, the ions' influence strength ranks as follows: Mg2+ > SO42− (coexisting with Mg2+) > Ca2+ > SO42− (alone) > Na+. This research provides new theoretical foundations and experimental data to support the development of smart water flooding in carbonate reservoirs.