Plant hormones are well known chemical signals that regulate plant growth, development, and adaptation. However, after comparative transcriptome and metabolite analysis, we found that the plant hormone abscisic acid (ABA) also affect the growth and metabolism of endophytic fungus Aspergillus nidulans. There were 3148 up-regulated and 3160 down-regulated genes identified during 100 nM ABA induction. These differentially expressed genes (DEGs) were mainly involved in: RNA polymerase and basal transcription factors; ribosome biogenesis, protein processing, proteasome, and ubiquitin mediated proteolysis; nucleotide metabolism and tri-carboxylic acid (TCA) cycle; cell cycle and biosynthesis of secondary metabolites. Production of mycotoxins, which have insect-resistance or anti-pathogen activity, was also changed with ABA induction. This study provides the first global view of ABA induced transcription and metabolite changes in endophytic fungus, which might suggest a potential fungus-plant cross-talk via ABA.