Salt stress is one of the most important stresses that affect coastal vegetation. A halophyte Carex pumila plays a crucial role in the maintenance of fragile ecosystems in coastal areas. Thus, understanding the mechanism of C. pumila responses to salt stress is a prerequisite for the conservation and utilization of this species. After treatment with 200, 300, 400, 500 mM NaCl for 60 h, C. pumila leaves displayed a decline in the relative water content and an increase in salt injury index. Osmolyte accumulation, as a function of osmotic adjustment, and antioxidant enzyme activities were maintained under salinity, even at a high NaCl concentration. High NaCl concentrations severely affected the photosystem II, the JIP-test indicated a significant decrease in performance indexes and quantum efficiencies and an increase in phenomenological fluxes. Metabolic analyses showed the changes of 39 metabolites, including 16 kinds of organic acids, 9 kinds of amino acids, 9 kinds of sugars, 3 kinds of sugar alcohols, and 2 amines. The identified metabolites were mainly involved in the glycolysis, pentose phosphate pathway, and tricarboxylic acids cycle.