Human spliceosome-associated factor 3, SART3, is a key factor in spliceosome recycling and engages with U6 small nuclear RNA (snRNA) to promote the formation of the U4/U6 small nuclear ribonucleoprotein complex. Unlike its counterpart U4/U6 snRNA-associated-splicing factor PRP24 (Prp24) from Saccharomyces cerevisiae, which uses four RNA recognition motifs (RRMs) for the U6 snRNA interaction, SART3 has two RRMs at its C terminus. Here, we demonstrate that SART3 binds U6 snRNA as a dimer, and four RRM subunits recognize the asymmetric bulge of U6 snRNA. SART3 RRMs adopt a tandem βαββαβ motif of the canonical RRM fold to interact with the U6 bulge region via a conserved electropositive surface. We identified the cognate U6 elements that specifically bind SART3 RRM1, which is distinct from the Prp24-U6 interactions in yeast. Our findings suggest a divergent RRM binding mechanism for U6 snRNA recognition during spliceosome assembly and recycling.