As a class of small non-coding RNA molecules, miRNA plays an important role in the molecular regulatory network of vertebrate bone metabolism. Normally, bone metabolism is referred to the modeling and remodeling processes in regulating calcium homeostasis, and scale tissue of fish is an ideal model for the study of bone metabolism due to its abundant quantity and easy acquisition. Salmon calcitonin (sCT) is a small peptide hormone isolated from the gills of salmonidae, which can inhibit the activity of osteoclasts to regulate calcium homeostasis of fish. In order to explore the regulatory mechanism of teleost bone metabolism, intraperitoneal injection of sCT was performed in Oncorhynchus mykiss juveniles and scales were collected 24 h after the injection. High-throughput sequencing technology and bioinformatics methods were performed to evaluate the effect of sCT on the miRNA expression profiles in scales. The results showed that 14 051 631 and 15 816 147 high quality miRNA sequences (18-26 nt) were obtained from the samples of the injection group (IG) and control group (CG), respectively, and 568 and 592 mature miRNA were identified in IG and CG scales, respectively. A total of 24 differentially expressed miRNAs (DEMs) including nine up regulated and 15 down regulated DEMs were identified. Eight miRNAs were randomly selected for quantitative real-time PCR (qRT-PCR) detection, and results were consistent with the RNA-Seq results. GO annotation and enrichment analysis revealed that the predicted target genes of DEMs were mainly annotated in the functions of metal ion binding, calcium ion binding, G protein coupled receptor signaling pathway, Wnt signaling pathway and classical Wnt signaling pathway; these genes were enriched in the negative regulation of NF-kappaB input into the nucleus, the negative regulation of interleukin-1 β (IL-1β) secretion and the binding of transforming growth factor β (TGF-β). KEGG enrichment analysis showed that the predicted target genes of DEMs were significantly enriched in toll-like receptor and estrogen-related signaling pathways. A total of six miRNA (omy-miR-29a-5p, omy-miR-30d-5p, omy-miR-125b-2-p3, omy-miR-138, omy-miR-199b-5p and omy-miR-200b) were identified, which could provide materials for future studies on the molecular mechanism of bone metabolism in teleosts.