Current indices of saline-alkaline (SA) tolerance are mainly based on the traditional growth and physiological indices for salinity tolerance and likely affect the accuracy of alfalfa tolerance predictions. We determined whether the inclusion of soil alkalinity-affected indices, particularly Ca2+, Mg2+, and their ratios to Na+ in plants, based on the traditional method could improve the prediction accuracy of SA tolerance in alfalfa, determine important indices for SA tolerance, and identify suitable alfalfa cultivars in alkaline salt-affected soils. Fifty alfalfa cultivars were evaluated for their SA tolerance under SA and non-SA field conditions. The SA-tolerance coefficient (SATC) for each investigated index of the alfalfa shoot was calculated as the ratio of SA to non-SA field conditions, and the contribution of SATC under different growth and physiological indices to SA tolerance was quantified based on the inclusion/exclusion of special alkalinity-affected indices. The traditional method, excluding the special alkalinity-affected indices, explained nearly all of the variation in alfalfa SA tolerance, and the most important predictor was the SATC of stem length. The new method, which included these special alkalinity-affected indices, had similar explanatory power but instead identified the SATC of shoot Ca2+/Na+ ratio, followed by that of stem length, as key markers for the field evaluation of SA tolerance. Ca2+, Mg2+, and their ratios to Na+ hold promise for enhancing the robustness of SA-tolerance predictions in alfalfa. These results encourage further investigation into the involvement of Ca2+ in such predictions in other plant species and soil types under more alkaline salt-affected conditions.