Salinity stress exerts a signifcant infuence on plant growth and productivity, underscoring the critical importance of comprehending how plants react to stressors. Rice, as a fundamental global food source, is particularly susceptible to salt stress during its early developmental stages. This study employs both qualitative (GC–MS) and quantitative (HPLC) analyses to assess metabolic compounds in the roots of fve rice varieties exhibiting varying degrees of salt tolerance during the seedling phase under NaCl-induced stress. The objectives are multifaceted: to ascertain alterations in these compounds and to delineate their metabolic profles across biochemical pathways. The fndings demonstrate that metabolite levels undergo fuctuations corresponding to NaCl concentration, and these fuctuations vary among the rice varieties examined. Specifcally, the study identifed 44 metabolites, comprising 23 organic acids, 18 sugars, and 3 amino acids. Furthermore, we quantifed the concentrations of several key compounds, which play a crucial role in osmotic balance, oxidative balance, and precursors for synthesizing other compounds, such as 9 sugars (mannose, ribose, rhamnose, glucuronic acid, glucose, galactose, xylose, arabinose, and fucose), 6 acids in the group of phenolic compounds (gallic, chlorogenic, cafeic, syringic, ferulic, and salicylic acids), two compounds (rutin and quercetin) and 12 organic acids (D-gluconic, 2-ketogluconic, nicotic, pyruvic, succinic, malic, itaconic, dimethyl fumarate, trans-aconitic, quinic, shikimic, and malonic) were elucidated. These fndings partly
contribute to understanding the mechanism and important compounds participating in the NaCl stress response mechanism. Those also illustrate the coordination and interrelationship of metabolites with metabolic and biosynthetic processes to help rice adapt to NaCl stress.