To evaluate the effects of hypersalinity and its fluctuation on the photo-physiological and the performances of marine “green tide” algae on salt tolerance, Ulva prolifera was selected as the experimental material. We set up three salinity conditions: salinity 25 as control (CK); treatment 1 (T1), salinity 30 for 3 d, then increased to salinity 35; treatment 2 (T2), salinity 35 for 6 d. The relative growth rate, the content of photosynthetic pigments, the photosynthetic and dark respiration rates and the gene expression levels of ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) and calmodulin (CaM) were measured. The results showed that compared with control groups, hypersalinity significantly inhibited the relative growth rates and photo-physiological performances. Both T1, T2 treatments inhibited the relative growth rates and net photosynthesis rates of U. prolifera, and the inhibition effects of T2 was much stronger than that of the former one. The effect of hypersalinity stress on the dark respiration rate was not significant, which also had no significant effect on the content of photosynthetic pigments and their ratio of photosynthetic pigments. However, the dark respiration rate was significantly increased and photosynthetic pigments was significantly decreased along with the algae grow up. And the gene expression levels of rbcL and cam were also affected by hypersalinity. U. prolifera cultured in T1 treatment showed better resistance to hypersalinity than T2 treatment after 3 d and 6 d. It showed that U. prolifera could adapt to hypersalinity when the salinity was increased gradually. These results could explain the adaptation ability on hypersalinity stress of U. prolifera at the period of green tide formed and low tide.