Jasmonate (JA) and gibberellins (GAs) exert antagonistic effects on plant growth and development in response to environmental and endogenous stimuli. This study investigated the mechanism underlying JA-mediated regulation of endogenous GA levels. JA treatment increased DELLA accumulation with reduction of endogenous GA levels. JA treatment decreased bioactive GA, significantly decreased the expression of GA biosynthesis genes, and increased the expression of AtGA2ox, a GA inactivation gene. Conversely, JA treatment did not significantly affect gene expression in the myc2 myc3 myc4 triple mutant, and MYC2 directly activates some AtGA2ox genes. Additionally, JA post-transcriptionally regulated AtGA3ox1 expression. We identified microRNA miR5998 as a GA3ox1-associated miRNA;its overexpression inhibited plant growth by suppressing GA3ox1 expression. Overall, our findings indicate that JA treatment inhibits endogenous GA levels and plant growth by decreasing the expression of GA biosynthesis genes and increasing the expression of GA inactivation genes via miR5998 and MYC2 activities.