The　great　selectivity　and　trans-cleavage　activity　of　clustered　regularly　interspaced　short　palindromic　repeats　(CRISPR)/Cas13a　had　been　coupled　with　high　amplification　efficiency　of　hybridization　chain　reaction　(HCR)　and　magnetic-assisted　enrichment,　high　sensitivity　of　electrochemiluminescence　(ECL)　detection　to　develop　an　ultra-sensitive　biosensor　for　microRNA-21　(miRNA-21).　The　CRISPR/Cas13a　was　used　to　recognize　target　RNA　with　high　specificity　and　performed　the　trans-cleavage　activity.　An　initiation　strand　was　generated　to　bind　to　the　probe　on　the　surface　of　nanomagnetic　beads　and　then　trigged　HCR　to　produce　long　double-strand　DNAs　(dsDNAs)　to　realize　signal　amplification.　Ru(phen)32+　can　be　inserted　in　the　groove　of　the　dsDNAs　and　acts　as　the　ECL　indicator,　which　can　be　separated　through　magnetic　enrichment　and　allowed　the　platform　to　reduce　the signal　background.　Under　the　optimized　conditions,　there　is　a　good　linear　correlation　between　the　ECL　intensity　and　the　logarithm　of　miRNA-21　concentration　in　the　range　1　fM–10 nM;　the　limit　of　detection　(LOD)　was　0.53　fM.　The　proposed　system　was　applied　to　detect　miRNA-21　from　the　urine　of　acute　kidney　injury　(AKI)　patients　with　good results.　Graphical　Abstract:　[Figure　not　available:　see　fulltext.]　©　2023,　The　Author(s),　under　exclusive　licence　to　Springer-Verlag　GmbH　Austria,　part　of　Springer　Nature.