To establish a minimum data set (MDS) for evaluating soil nutrient quality in genuine medicinal material producing areas, this study focused on soils of four medicinal plants: Paeonia lactiflora, Paeonia suffruticosa, Chrysanthemum morifolium, and Angelica dahurica, located in Qiaocheng District, Bozhou City. Utilizing 17 physicochemical indicators derived from 125 samples, key indicators were selected through principal component analysis to construct the MDS, allowing for a systematic evaluation of differences in soil nutrient quality among various medicinal plant cultivation areas. The results revealed significant variations in soil nutrient characteristics: Paeonia lactiflora fields exhibited higher total levels of nitrogen, potassium, copper, and zinc, but mild deficiency in available potassium (AK); Paeonia suffruticosa fields had the lowest concentrations of AK, total manganese, total copper, and total zinc; Chrysanthemum morifolium fields displayed reduced total levels of calcium, copper, and zinc, yet elevated AK; whereas Angelica dahurica fields showed the highest amounts of organic matter (SOM), alkali-hydrolyzable nitrogen (AN), and available phosphorus (AP), but suffered from severe AK deficiency. The MDS indicators varied by medicinal plant type and demonstrated a significant positive correlation with the total data set (TDS) in evaluation results (R² = 0.686-0.821). The soil nutrient quality index based on the MDS was ranked as follows: Paeonia lactiflora (0.503) > Angelica dahurica (0.494) > Paeonia suffruticosa (0.483) > Chrysanthemum morifolium (0.414). In conclusion, the MDS effectively represents the TDS in evaluating soil nutrient quality in genuine medicinal material producing areas. It is recommended that categorized management and precision fertilization be implemented in different medicinal cultivation areas to enhance soil nutrients and promote sustainable development.