This study investigates the response mechanisms and alterations in secondary metabolite content of Nekemias grossedentata (N. grossedentata), characterized by three distinct genetic backgrounds when cultivated in native soil, dolomite-adhered soil, and limestone-adhered soil. Our findings indicate that N. grossedentata specimens originating from YNHH, GXJX, and YNGN demonstrate the ability to thrive in dolomite and limestone soils, which possess total calcium contents of 34.94 g/kg and 75.60 g/kg, respectively. Moreover, the primary functional components, such as dihydromyricetin, myricetin, and myricitrin, exhibited distinct patterns of variation, with myricitrin displaying an increasing trend as soil calcium content increased. Additionally, stress resistance indicators, including the variations in chlorophyll and soluble sugars, are associated with the genetic background. Furthermore, the calcium content in the leaves increases in correlation with the rising calcium levels in the soil. In summary, the physiological condition of N. grossedentata was sensitive to calcium stress, and plants with varying genetic backgrounds exhibited significant differences in their responses to soil conditions with differing calcium levels. This study offers a theoretical foundation for utilizing N. grossedentata in the remediation of rocky desertification.