Phytohormones play a role in regulating microalgae cells tolerance to adversity. This paper examines the effects of different temperatures (20 °C, 25 °C, 30 °C and 35 °C) on the physiological characteristics and endogenous phytohormones of the Isochrysis Zhanjiangensis (IZ) and its mutagenic strain (3005). The results showed that the endogenous phytohormones indole acetic acid (IAA) and jasmonic acid (JA) exhibited significant differences (P<0.05) between the two strains. The addition of 0.5 mg·L-1 exogenous JA inhibitor ibuprofen (IBU) improved cell growth of IZ, and was extremely effective in the accumulation of polysaccharides, which accounted for 33.25 %. Transcriptomic analyses revealed that genes involved in photosynthesis, such as PetC and PsbO, exhibited significantly elevated expression of the strain IZ, while the pathways related to JA synthesis may be the factor affecting microalgae temperature tolerance. This study provides a theoretical foundation for elucidating the underlying mechanisms and potential applications for high temperature tolerance in IZ.