Fraxinus Mandshurica Rupr. is one of the major hardwood species in Northeast of China and is a valuable timber forest. However, drought in the seedling stage severely restricts its growth and wood formation. In this study, we used defense signaling molecules, salicylic acid (SA), zinc oxide nanoparticles (ZnO-NPs), and plant endophytes (FMR21, Fungal sp. and FMR22, Alternaria tenuissima) to explore their role for drought tolerance in F. mandshurica seedlings. The results showed that 50mg/L SA, 20-30mg/L ZnO-NPs, endophytic fungi FMR21+FMR22 have improved significantly the drought resistance. The plant height and root activity of seedlings treatment with SA+FMR21+FMR22(SA+FMR) soaked seeds treatment were increased by 31.25% and 82.95%, respectively. The net photosynthetic rate and the lignin content were increased by 2.21 times and by 1.66 times. Nitrogen content in leaf was increased by more than 60% after spraying 50mg/L SA and SA+FMR fungal solution, and the contents of flavonoids, polyphenols, and lignin in stem skin and leaves were effectively increased by more than 20% compared with the control. The above results were verified by field experiment in arid area of Heilongjiang Province. Further, the transcriptome analysis of SA-induced F. mandshurica seedlings showed 1343 differential genes, of which 764 were up-regulated and 579 down-regulated. The differential genes were mainly concentrated in plant-pathogen interaction, MAPK pathway, and phenylpropane pathway. And found that, under drought stress, spraying SA enhanced the expression of WRKY transcription factor genes and the expression of NPR1, TGA and four 4CL genes, thus promoting the accumulation of secondary metabolites and stress resistance substances, which may indicate the reason why SA improves drought resistance in F. mandshurica. This study provided establishment of drought-resistant cultivation technology and important marker genes for early breeding of drought-resistant varieties of F. mandshurica.