In order to study the effects of the main agronomic traits of isatis indigotica on the yield of medicinal materials under mulched drip irrigation based on water deficit (WD), the WD treatment of isatis indigotica in the vegetative growth and fleshy root growth period was carried out, and ten main agronomic traits of isatis indigotica were measured and calculated. Correlation analysis, regression analysis and path analysis were used to analyze the correlation between various agronomic traits. The results showed that the WD treatment had a certain degree of influence on the main agronomic traits of isatis indigotica, with a coefficient of variation (CV) of 5.45%~17.19%, and the CV values of folium yield and radix yield were 13.14% and 16.28%, respectively. There was a significant positive correlation（P<0.05）between the coefficient of folium and radix yields and the remaining agronomic traits except for the root-to-shoot ratio. A regression model between the folium and radix yields and agronomic traits was established. With the statistical tests, it was found that both of them reached extremely significant levels（P<0.01）, and the coefficients of determination were 0.996 and 0.971, respectively. Through the path analysis, the main agronomic traits affecting the yield of folium were plant height(0.498) and main root length(0.630), the key agronomic traits affecting the yield of radix were leaf length(0.698). Therefore, in the cultivation process of isatis indigotica, the WD treatment can improve the allocation of biomass in each part of the plant under drought stress, increase the plant height, leaf length and main root length, which ultimately contributes to the formation of yield.