In our previous study, aurone compound were found in the n-butanol fraction of Sterculia quadrifida leaves. The aurone compound (compound 1) had high cytotoxic activity in cell lines with IC50 values of 4.05, 12.53, 15.38, and 25.91 μg/mL in 4T1, MCF7, MDA-MB-435, T47D, respectively. In this study, we performed the MMP-9 enzyme inhibition test with FRET assay, and to deepen the mechanism of action of the compounds use molecular docking and molecular dynamics. The results showed that compound 1 had the MMP-9 enzyme inhibition of 91.23% and IC50 48.27%. Furthermore, molecular docking and molecular dynamic simulation suggest compound 1 interacts firmly and stably at the enzyme catalytic site. In conclusion, this study can provide important information on the development of herbal medicines that are potentially cancer drugs.