Palmella stage is critical for some unicellular algae to survive in extreme environment conditions. The halotolerant algae Dunaliella salina is a good single-cell model for studying plant adaptation to high salinity. We found 35 salinity-responsive phosphoproteins were involved in multiple signaling and metabolic pathways upon palmella formation. The patterns of protein accumulation exhibited changes, including dynamics of cytoskeleton and cell membrane curvature, accumulation and transport of exopolycsccharides, photosynthesis and energy supplying (i.e. photosystem II stability and activity, cyclic electron transport, photorespiration, and C4 pathway), nuclear/chloroplastic gene expression regulation and protein processing, reactive oxygen species homeostasis, and salt signaling transduction. To our knowledge, this study of protein post-translational modifications regulation toward understanding the mechanism of algae palmella formation has not been reported before.