Abstract: Salt stress is one of important ecological factors influencing survival of desert soil algae. Palmellococcus Chod. is a kind of green algae widely distribute in biological soil crusts and is able to accumulate red pigment (astaxanthin) and oil drops, and the algae has displayed especial physiological nature and potential value of application. Currently, studies on physiology, cellular structures and pigment accumulations of Palmellococcus sp. were relatively scarce. In this study, Palmellococcus sp., isolated from desert algal crusts, was selected for experiment material. Physiological effects of salt stress on the algal cells were investigated by measuring biomass (expressed as chlorophyll a), PS activity Ⅱ (Fv/Fm), intracellular production of water-soluble proteins and saccharides, MDA contents as well as the activities of SOD and CAT. The results showed that salt stress resulted in an obvious decrease in biomass and PSⅡ activity of the treated cells compared to the control cells. It also indicated that intracellular production of water-soluble saccharide and water-soluble proteins were all comparatively greater in the treatment cells than the control cells. Moreover, salt stress had a significantly deleterious effect on membrane lipid superoxide as assessed by measurement of MDA content, and SOD and CAT activities also presented obvious increases as compared to the control. At the same time, it showed from this study that cellular structures and morphological characteristics of Palmellococcus sp. were found to keep intact and clear in the control condition, and there was plentiful lipid body accumulation at growth anaphase of the control culture. However, gradual destruction property in cellular structures were observed from Palmellococcus sp. subjected to salt stress, and synchronously starch and lipid body accumulation were also detected in the treated cells. Furthermore, unintelligible cellular structures and disappearance of cellular organs were observed from Palmellococcus sp. under salt treatment, and plasmolysis and vacuolization were appeared in the treated algal cells. The research results maybe provided us some significative findings for better understanding physiological adaptation, morphological changes and pigment accumulation of Palmellococcus sp. when subjected to salt stress environment, and simultaneously provided us many experimental data for further researches and applications about the green algae.