NapRNAdb is the first database dedicated to napRNAs that allows researchers to profile napRNA transcriptomes across 40 species. This resource integrates 3,0708 napRNAs derived from human and mouse NAP-seq with their expression profiles in multiple biological models, comprising 10,16 ACA-napRNAs, 297 CD-napRNAs, 2,302 Pol3-napRNAs, 157 polyA-pocket-ACA-napRNAs, 1,536 sliRNAs, 57 snotrons, 55 misRNAs, and 25,288 others. Leveraging evolutionary conservation analysis, NapRNAdb cost-effectively identifies 197,345 napRNAs spanning 8 categories in 38 species, with secondary structure for each molecule. Critically, NapRNAdb delivers the powerful "PreTool" module for efficiently evaluating the potential of any target sequence to be processed into napRNAs via sequence similarity analysis. It also supports gene queries to verify participation in nascent napRNA formation. Furthermore, it systematically deciphers interaction networks linking napRNAs to RNA modifications, RNA-binding proteins and disease-associated single nucleotide variants (SNVs). Overall, NapRNAdb provides interactive interfaces to explore transcriptional, structural, expressional, and functional landscapes for napRNAs, empowering comprehensive dissection of their biology and accelerating mechanistic insights into this field.