RNA secondary structure (RSS) of primary microRNAs (pri-miRNAs) is a key determinant for miRNA production. Here we report that RNA helicase (RH) Brr2a, best known as a spliceosome component, modulates the structural complexity of pri-miRNAs to fine tune miRNA yield. Brr2a interacts with microprocessor component HYL1 and its loss reduces the levels of miRNAs derived from both intron-containing and intron-lacking pri-miRNAs. Brr2a binds to pri-miRNAs in vivo and in vitro. Furthermore, Brr2a hydrolyses ATP and the activity can be significantly enhanced by pri-miRNAs. Consequently, Brr2a unwinds pri-miRNAs in vitro. Moreover, Brr2a variants with compromised ATPase or RH activity are incapable of unwinding pri-miRNA, and their transgenic plants fail to restore miRNA levels in brr2a-2. Importantly, most of tested pri-miRNAs display distinct RSS, rendering them unsuitable for efficient processing in brr2a mutants vs Col-0. Collectively, this study reveals that Brr2a plays a non-canonical role in miRNA production beyond splicing regulation.