RNA-targeting small molecules have the potential to modulate RNA function and offer possible applications in drug development. However, their molecular recognition mechanisms remain poorly understood due to limited structural insights. To advance our understanding of how these small molecules interact with their target RNAs, it is essential to identify and analyze RNA-small molecule complexes that can serve as models for structural studies. In this study, we identified novel RNA motifs that bind selectively to the small molecule naphthyridine-azaquinolone (NA), previously known to interact with CAG/CAG motif in DNA. Using different methods, including surface plasmon resonance (SPR), thermal melting, and cold-spray ionization mass spectrometry, we investigated the interaction between NA and the RNA motifs. Furthermore, we determined the solution structure of the NA-RNA complex, revealing a distinct binding mode from its DNA interaction. The findings in this study provide molecular-level insight into RNA-small molecule recognition and highlight the potential of NA as a scaffold for developing RNA-targeting small molecules.