Miscanthus lutarioriparius, an endemic species of Miscanthus (Poaceae) in China, is considered to be one of the most promising second-generation energy crops that could grow in the condition of salinity stress. Studying photosynthetic traits of M. lutarioriparius under salinity stress can uncover the adaptability and foundation for selecting stress-resistant energy crops. In this study, several M. lutarioriparius populations were planted with randomized block design in the coastal saline experimental field in Dongying( ~7% in sanility), Shandong Province. After two growing seasons, we randomly sampled 50 individuals from five populations, correspondingly performed their photosynthetic analysis and RNA-Seq. We found the photosynthetic rate (A) of these individuals ranged from 19.19 to 42.80 μmol m^-2 s^-1, at an average of 32.58 μmol mm^-2 s^-1. The mean of stomatal conductance (g_s) was 0.56 mol m^-2 s^-1. The water use efficiency was mainly impacted by transpiration rates. The candidate genes related to photosynthetic rate mainly involved in photosynthesis, osmoregulation, abiotic stress and signal transduction. The stress-resistance genes had a significant effect on photosynthesis under long-term salinity stress, and most of the candidate genes were potentially beneficial for M. lutarioriparius to adapt to the stressful environment. Therefore, we inferred that M. lutarioriparius did not achieve adaptation by directly altering the expressions of the photosynthetic key genes, but by repairing and regulating the functions of key genes in order to maintain normal photosynthesis.