In this study，plug seedling experiment was carried out to clarify the effect of different types of nitrogen fertilizers on substrate seedling，using amino acid nitrogen fertilizer(AA)，chemical ammonium nitrogen fertilizer(CF)and seedling substrate from the Chinese traditional medicine waste，and the growth index parameters of seedlings were analyzed.Results showed that both types of nitrogen fertilizer significantly increased chlorophyll SPAD value(6.4% and 8.4%)and seedling stem diameter(2.5% and 3.8%).Compared with the control and CF treatments，AA significantly improved the strong seedling index(16.4% and 20.1%)，the underground dry weight(17.9% and 22.2%)and the aboveground dry weight(17.4% and 18.7%)；also significantly increased the root surface(13.3% and 18.5%)，average diameter(38.9% and 25.0%)，root length(10.4% and 31.5%)and root volume(6.3% and 13.3%).Compared with the control，CF had not significantly effect on strong seedling indexs the dry weight of seedlings aboveground and underground，but decreased root surface and reduced root length per volume(P<0.05).Furthermore，AA significantly increased the percentage of fine root in the whole root structure. In details，root surface，root length and root volume of fine root raised by 22.9%，20.8% and 49.6%，respectively.The results indicated that AA application in seedling substrate may change the root characteristics of morphology and structure to achieve higher seedling index.This work provides technical support for fertilizer selection in the process of plug substrate seedling.