In this study, the colonies of N. flagelliforme with different water loss treatments were used as the research material, and fully waterabsorbent state was used as a control. Highthroughput sequencing and qRTPCR techniques were used to detect the differential expression of photosynthesisrelated genes under drought stress, and the changes of photosynthetic pigments were also detected. The results showed that: (1) 113 photosynthesisrelated genes were differentially expressed under different degrees of drought stress, and 44, 74 and 91 photosynthesisrelated genes were differentially expressed in 30%, 75% and 100% dehydrated colonies, respectively. (2) The contents of phycobilin, chlorophyll and carotenoid decreased gradually with the drought intensifies, the Rubisco activity increased at first and then decreased but the activity of GAPDH decreased with the increase of drought stress. The results showed that N. flagelliforme regulates photosynthetic activity through the differential expression of photosynthesisrelated genes to adapt to drought stress. The research provides reference value for further research on the drought stress response mechanism of N. flagelliforme and lays a foundation for further understanding of the photosynthetic mechanism of N. flagelliforme drought tolerance.