The morphological indexes of the Scuophularia ningpoensis seedlings including the longth, diameter and weight were measured, clustering analysis was used to set up the standard quality grading of seedlings of S. Ningpoensis by SPSS. Field experiment was carried out to measure the indicators of plants growth and development, the yield and the quality. The results showed that the growth and yield of class I seedlings were better than those of class II and III. The content of main active ingredients was affected barely by seedlings classification. To ensure the quality, class II seedlings or above should be used for plantation. The established quality classification standard of S. ningpoensis seedlings was scientific and feasible, and provides the basis for the standardized cultivation of S. ningpoensis.