Zearalenone (ZEN) is one of the most common mycotoxin contaminants in food. For food safety, an efficient and environmental-friendly approach to ZEN degradation is significant. In this study, an Aspergillus niger strain, FS10, was stimulated with 1.0 μg/mL ZEN for 24 h, repeating 5 times to obtain a stressed strain, Zearalenone-Stressed-FS10 (ZEN-S-FS10), with high degradation efficiency. The results show that the degradation rate of ZEN-S-FS10 to ZEN can be stabilized above 95%. Through metabolomics analysis of the metabolome difference of FS10 before and after ZEN stimulation, it was found that the change of metabolic profile may be the main reason for the increase in the degradation rate of ZEN. The optimization results of degradation conditions of ZEN-S-FS10 show that the degradation efficiency is the highest with a concentration of 104 CFU/mL and a period of 28 h. Finally, we analyzed the degradation products by UPLC-q-TOF, which shows that ZEN was degraded into two low-toxicity products: C18H22O8S (Zearalenone 4-sulfate) and C18H22O5 ((E)-Zearalenone). This provides a wide range of possibilities for the industrial application of this strain.