Brassica napus L. (rapeseed), an oil crop widely cropped in arid and semi-arid areas of Xinjiang, China, is susceptible to ion toxicity under saline-alkaline conditions. Exogenous Ca2+ application can improve crop stress tolerance, but its effect on the ion migration and accumulation of alkaline-stressed rapeseed is still unclear. Therefore, in this study, the effects of different concentrations of CaCl2 (CK, 0%, 0.25%, 0.5%, 1% and 2%) solution foliar on the ionic homeostasis of salt-tolerant rapeseed variety "Huayouza 62" and salt-sensitive rapeseed variety "Xiangyou 15" under NaHCO3 stress were studied. The results showed that NaHCO3 stress inhibited rapeseed Ca2+ uptake in stems and leaves, resulting in K+ and Na+ imbalance in various tissues, the plasma membrane permeability and MDA content were significantly increased. The Non-invasive Micro-Test technology (NMT) detection found that the influx of Na+ and the efflux of K+ and Ca2+ in "Xiangyou 15" mesophyll cells were more significant than those in "Huayouza 62" under NaHCO3 stress, and the growth and development were significantly inhibited. However, after foliar spraying concentration was 0.5% CaCl2 solution, the ion imbalance-induced membrane damage was significantly alleviated, the influx of Na+ and the efflux of K+ and Ca+ in mesophyll cells were inhibited, and the K+ and Na+ homeostasis was maintained in different tissues, this effect was particularly prominent in the stems and leaves of "Huayouza 62" and roots of "Xiangyou 15", and it promoted the growth and development of rapeseed seedlings. Therefore, foliar spraying with an appropriate concentration of Ca2+ could promote the K+ and Na+ homeostasis and improve salt tolerance of alkali-stressed rapeseed seedlings. This study will deepen our understanding of how exogenous Ca2+ application regulates alkaline-stressed rapeseed ionic homeostasis, and provide a method for improving the adaptability and growth of rapeseed in arid areas.