Abstract: The excessive growth of green algae Ulva, including Ulva flexuosa, causes the outbreak of green tide in coastal area. These green algae with great fertility grow in the intertidal zone and are often affected by light, temperature and other ecological factors. At the same time, they have high tolerance to various abiotic factors. The growth and reproduction of Ulva flexuosa require the accumulation of organic matter, and the efficient accumulation of organic matter is the internal cause of its eruption. In this study, the response of photosynthetic system of U. flexuosa to the changes of light and temperature was investigated at molecular level. The adjustment mechanism of Ulva flexuosa was explained on these aspects: electron transfer of the initial reaction, photophosphorylation and finally carbon fixation. The whole experiment involved two factors, a total of nine experimental samples Nine sets of transcriptome data were obtained and the differential expression genes were mainly analyzed. First, the chlorophyll synthesis related genes down-regulated under high temperature and light 30℃, 400 μmol/(m²·s). Second, the carotenoid synthesis related genes down-regulated under low temperature and high light 4℃, 400 μmol/(m²·s). Third, electron transport chain, CF₁F₀-ATP synthase and other genes had weak ability in resistance to temperature and light, wherein the expression levels of related genes in all experimental groups showed a downward trend. Fourth, under high temperature environment, the influence of high light on U. flexuosa was more significantly (Q1). In low temperature environment, the effect of low light was more significantly (Q9). Finally, the expression of light harvesting complex gene up-regulated. The results showed that U. flexuosa had a certain tolerance to temperature and light changes, wherein temperature had a great influence on the photosynthetic gene of U. flexuosa, especially at high temperature and strong light. In this experiment, two ecological factors with the most significant effects on photosynthesis were integrated to conduct the experiment, which is helpful to fully understand the response mechanism of the photosynthesis of U. flexuosa, to accurately understand U. flexuosa outbreak in the light of the different sea temperature under the condition of the photosynthesis system coping mechanisms, for further analysis in the process of the green tide outbreaks physiological activity to support the main species.