Pyropia haitanensis lives in the mid-high tide area, and will suffer from periodic strong light stress after the ebb tide. However, the thallus can quickly return to normal growth after high tide rehydration, which indicates P. haitanensis has a strong ability to resist high light. To explore the mechanism of high-light resistance, two new strains of P.haitanensis with significant differences in high light resistance were selected for the experiment (green strain: 9-Ⅳ; orange strain: WO141-3). The physiological indexes such as photosynthetic rate and antioxidant enzyme activity of the two strains under high light stress were measured, the differential transcriptional expression profiles of the two strains were constructed and the key pathways and genes regulating the high light resistance of P. haitanensis were obtained by combining with fluorescence quantitative analysis technology. Result showed that under high light stress, the content of MDA in the thallus of the two P. haitanensis strains increased significantly, the expression of some genes in the photosystem was appreciably decreased, and the photosynthetic capacity of the algae was decreased noticeably. Further analysis showed that the WO141-3 strain had stronger high light resistance after 1 h of high light treatment, while the 9-Ⅳ strain had stronger high light resistance after 4 h of treatment. The main reasons for this difference were: Under high light stress for 1 h, the WO141-3 strain had higher reactive oxygen species scavenging ability and stronger non-photochemical quenching ability, lower pigment content and light-harvesting protein gene expression.Under high light stress for 4 h, 9-Ⅳ strain had stronger ability of scavenging reactive oxygen species and stronger non photochemical quenching, lower pigment content and light harvesting protein gene expression. Studies have shown, P. haitanensis can respond to high light stress by activating non-photochemical quenching mechanism and antioxidant system, reducing pigment content and light harvesting protein gene expression, so as to avoid excessive light damage and oxidative damage. The results of this study laid a theoretical foundation for elucidating the mechanism of high light tolerance of P. haitanensis.