In order to understand the response mode of the main chemical compounds to salt-stress, the chemical compositions in leaves and roots of NaCl-treated Limonium bicolor (Bag.) Kuntze, a medicinal halophytic plant with efficacy of blood enriching and hemostasis, were determined by UPLC-Q-TOF-MS2 and HPLC, and compared to the control, the expression analysis of chalcone synthase (CHS) gene under salt-stress was also carried out by quantitative real-time PCR. As a result, eleven chemical constituents including triethyl citrate (1), gallic acid (2), vanillic acid (3), vanillic acid derivative (4), vanillic acid-hexose (5), N-(2-carboxyethyl) iminodiacetic acid (6), epigallocatechin gallate (7), myricetin-3-O-glucoside/galactoside (8), myricetin-3-O-rhamnoside (9), quercetin-3-O-rhamnoside (10) and myricetin-3-O-(O-galloyl)-rhamnoside (11) were identified, and showed that NaCl-stress can induce accumulation changes of these compounds. Among them, compound 9 showed the highest abundance both in leaf and root of L. bicolor, which can be markedly enhanced in root by NaCl-stress. CHS gene was sensitive to NaCl-stress, its expression level was up-regulated in leaf while inhibited in root by NaCl-stress. These results will provide references for further research of the directional induction of medicinal active ingredients and the salt response mechanism of secondary metabolism in medicinal halophyte L. bicolor.