## 1 Introduction  
Soil salinization represents a severe abiotic stress and is one of the significant obstacles to plant growth [1]. More than 7% of the Earth's land and 20% of irrigated land has already been affected by salinization globally [2], and the affected area continues to expand. China possesses approximately 33 million hectares of saline soils, ranking as the third-largest globally [3]. The cause of soil salinization is attributed to the excessive accumulation of ions, particularly Na\({}^{+}\) and Cl\({}^{-}\)[4]. Therefore, understanding crop responses to salt stress, especially NaCl stress, is critical for enhancing crop salt tolerance.  
Salt stress in plants induces multiple forms of stress [5,6], including osmotic, ionic, oxidative, and nutrient imbalances, which leads to the accumulation of reactive oxygen species (ROS) that cause cellular damage [7]. To mitigate these effects, plants have developed both enzymatic and non-enzymatic antioxidant defense systems [8]. Enzymatic systems combat ROS by enhancing the activity of enzymes like superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) [9], while non-enzymatic systems rely on antioxidants such as glutathione (GSH), phenolic compounds (PhOH), and flavonoids [10]. Flavonoids, in particular, play a crucial role in plant responses to salt stress by scavenging ROS and protecting cells from damage [11,12]. For instance, salt-tolerant soybean varieties, like FQ07, accumulate higher levels of flavonoids under salt stress, which helps mitigate oxidative damage and improves stress resistance [13]. Similarly, salt stress has been shown to influence the phenylpropanol and flavonoid biosynthesis pathways in other crops such as cauliflower bean [14], and in _Lycium barbarum_, flavonoids help alleviate ROS-induced damage, enhancing both salt tolerance and overall plant quality [15]. Thus, both enzymatic and non-enzymatic antioxidants are crucial for managing ROS accumulation, which is essential for maintaining healthy plant growth under stressful conditions [16].  
_Astragalus membrananccus_ (Fisch.) Bge. var. _mongholicus_ (Bge.) Hsiao is a perennial herb of the genus _Astragalus_ in the family _Leguminosae_, widely utilized worldwide for its high medicinal value [17]. Inner Mongolia is a major producing area of _A.__mongholicus_, but the predominance of saline soils in the region significantly restricted the development of the regional industry. Interestingly, saline soils, though generally unsuitable for plant growth, were conducive to the accumulation of medicinal components [18]. If saline-tolerant varieties meeting medicinal standards could be domesticated, this would address the technical bottlenecks limiting the _Astragalus_ industry in Inner Mongolia. However, the salt tolerance mechanism of such species remained unexplored, necessitating molecular biology studies and other analytical methods. In recent years, combined metabolome and transcriptome analyses have been widely applied to investigate salt stress responses in crops such as cotton [19], tamarisk [20], and sorghum [21]. _A.__mongholicus_ exhibited some degree of salt tolerance under stress, but its underlying mechanisms required further exploration. This study employs two _A.__mongholicus_ germplasms with differing salt tolerance levels, based on the analysis of their morphological and physiological responses to salt stress. By identifying differential metabolites (DAMs) and differentially expressed genes (DEGs), this research aims to elucidate the key metabolic pathways involved in salt stress responses. The findings will not only enhance our understanding of the molecular mechanisms underlying salt tolerance in _A.__mongholicus_ but also provide a scientific foundation for its cultivation and industrial application in saline environments, addressing key challenges in the industry and facilitating the resolution of bottlenecks.