The Minimum Data Set (MDS) is an effective way to improve understanding of the assessing soil quality and understanding of the heterogeneity of soil quality and encourage the adaption of proper agriculture practice. However, a suitable evaluation method of the soil quality of Astragalus mongholicus and ecological link between this and the active ingredients, including astragalosides (I, II, and IV) and calycosin, was poorly known in the main cultivation region in China. This study selected 22 soil indicators and 4 active ingredients factors and used principle component analysis to construct MDS to determine a comprehensive set of indicators for assess soil quality and established the agriculture practice in the main cultivation regions of A. mongholicus. Our results indicated that the quality of A. mongholicus, based on the quality score of the active ingredients from the PCA, increased with an increase in the soil quality. The five soil factors, soil organic matter(SOM), soil total calcium(STCa), soil total gallium(STGa), soil total borom(STB), and soil total magnesium(STMg), were obtained within 10% of the highest score of the total soil scores and r < 0.5 by the MDS method. In addition, the assessment quality index (AQI) of A. mongholicus was obtained from the score and contribution in the PCA and the soil quality index (SQI) was assessed by the MDS method. Interestingly, SOM, STCa were the limiting factors influencing the astragaloside II and IV content. Additionally, a significantly positive correlation was found between the SQI (r = 0.372, P < 0.01), pH (r = 0.260, P < 0.05) and AQI. The findings of this study provided a novel approach for the soil quality evaluation of A. mongholicus and the SOM, STCa and pH may be an effective and practical tool to achieve a strategic regional goal, with respect to a sustainable high quality of A. mongholicus.