Soil salinization is one of most crucial environmental problems around the world and negatively affects plant growth and production. Carex rigescens is a turfgrass with favorable stress tolerance and great application prospect in salinity soil remediation and utilization; however, the molecular mechanisms behind its salt stress response are unknown. We performed a time-course transcriptome analysis between salt tolerant ‘Huanghua’ (HH) and salt sensitive ‘Beijing’ (BJ) genotypes. Physiological changes within 24 h were observed, with the HH genotype exhibiting increased salt tolerance compared to BJ. 5764 and 10752 differentially expressed genes were approved by transcriptome in BJ and HH genotype, respectively, and dynamic analysis showed a discrepant profile between two genotypes. In the BJ genotype, genes related to carbohydrate metabolism and stress response were more active and ABA signal transduction pathway might play a more important role in salt stress tolerance than in HH genotype. In the HH genotype, unique increases in the regulatory network of transcription factors, hormone signal transduction, and oxidation-reduction processes were observed. Moreover, trehalose and pectin biosynthesis and chitin catabolic related genes were specifically involved in the HH genotype, which may have contributed to salt tolerance. Moreover, some candidate genes like mannan endo-1,4-beta-mannosidase and EG45-like domain-containing protein are highlighted for future research about salt stress resistance in C. rigescens and other plant species. Our study revealed unique salt adaptation and resistance characteristics of two C. rigescens genotypes and these findings could help to enrich the currently available knowledge and clarify the detailed salt stress regulatory mechanisms in C. rigescens and other plants.