Global warming increases seawater temperature, causing high temperature stress to marine organisms, including algae. This study aimed to explore the global proteomic response of Sargassum fusiforme under high temperature stress. Sargassum fusiforme seedlings were cultured in natural seawater for 24 hr and subjected to different temperatures (22°C, control group; 27°C and 32°C, high temperature stress group) for 1, 3, 5 and 7 days. Changes in their membrane lipid peroxidation after high temperature stress were investigated. Proteomic changes in the air bladders of S. fusiforme were analysed using isobaric tags for relative and absolute quantification, along with liquid chromatography-tandem mass spectrometry. Data were analysed using bioinformatics methods. Results showed that high temperature stress destroyed the cell membrane of the air bladders. Further, 28 and 53 differentially expressed proteins (DEPs) were found in the 27°C and 32°C treatment groups respectively. These DEPs were mainly involved in glycolysis, single-organism catabolism, purine nucleoside diphosphate metabolism and carbohydrate catabolism. In addition, DEPs were significantly enriched in 10 pathways, such as glycolytic process, biosynthesis of antibiotics, ribosome, biosynthesis of secondary metabolites and biosynthesis of amino acids. Proteomics analyses indicated that proteins associated with synthesis, folding, degradation, photosynthesis and energy and carbohydrate metabolism are differentially expressed under high temperature stress and normal conditions.