AbstractSoil salinization is a major environmental threat to the entire terrestrial ecosystem. Lichens arose from the symbiosis of fungi and algae or cyanobacteria. They have a high tolerance to various extreme environments, including adaptation to saline‐alkali habitats. Thus, lichens are pioneer species on saline‐alkali soil. However, the separate resilience of the two symbiotic partners under saline‐alkali conditions remains insufficiently understood. In this study, two representative symbiotic algae, Diplosphaera chodatii and Trebouxia jamesii, were studied for their physiological response to the saline‐alkali stress by adjusting different concentrations of NaHCO3, together with their respective symbiotic fungi Endocarpon pusillum (terricolous lichen) and Umbilicaria muhlenbergii (saxicolous lichen). The results indicate that cell growth rate and biomass in all four cultures decreased in alkali‐alkaline substrate, while cellular activities and ultrastructure were affected to a distinct extent. Compared with the symbiotic fungi, the algae were found to be more active in coordinating oxidative stress and lipid peroxidation damage under the saline‐alkali stress. The antioxidant system of the alga was especially shown as a key adaptive trait and it provides an important strategy for species survival and persistence in arid saline‐alkali desert. The specific survival ability of the lichen symbiosis relies on the stress resilience advantages of the symbiotic partners in combination. Our study provided new insights into understanding the adaptation of lichen symbiosis to desert saline‐alkali soil, and the potential of lichen symbiotic algae in the future desert ecological restoration.