Eucommia ulmoides Oliver is a valuable medicinal plant renowned for its diverse, health-promoting compounds. However, its slow growth and low content of bioactive constituents limit its pharmaceutical development. In this study, a novel endophytic fungus exhibiting multiple in vitro plant growth-promoting traits was isolated from E. ulmoides leaves and identified as Aspergillus sp. Y232. We explored the effects of Y232 on plant growth and the accumulation of characteristic bioactive compounds in E. ulmoides along with the underlying mechanisms. Results revealed that Y232 significantly enhances seed germination and promotes seedling growth, with increases in the content of characteristic iridoids, phenolics, lignans, and flavonoids ranging from 16.6% to 37.4%. Additionally, Y232 inoculation resulted in elevated activities of antioxidant enzymes (SOD, POD, and CAT) and upregulation of key enzyme genes (PAL, 4CL, CHI, and HCT) involved in phenylpropanoid biosynthesis. These findings indicate that Y232 may activate the antioxidant defense system and stimulate phenylpropanoid metabolism, contributing to increased secondary metabolite accumulation. This study underscores the beneficial role of Aspergillus sp. Y232 as an eco-friendly alternative to chemical fertilizers, promoting the growth and quality of economically significant medicinal plants.