Background Ovary is an important reproductive organ for poultry. MicroRNA (miRNA) is a highly conserved class of small non-coding RNA that function in a specific manner to post-transcriptionally regulate gene expression in organisms. Currently, miRNA has been studied extensively but research on duck ovarian tissue is relatively rare. Thus, in this study, we performed the first miRNA analysis of ovarian tissues in Leizhou black ducks with low and high rates of egg production. Method: Using high-throughput sequencing technology, miRNA library was constructed to obtain miRNA expression profile; differentially expressed miRNAs were screened, to predict miRNA target genes. Results A total of 29 differentially expressed miRNAs were obtained from the miRNA library, of which 7 were up-regulated and 22 were down-regulated. Verification of 12 randomly selected miRNAs, using RT-qPCR technology showed the results are consistent with the sequencing data, indicating that the sequencing results are reliable. The GO enrichment and KEGG pathway enrichment analysis of differential miRNAs showed that target genes were significantly enriched in signal pathways related to ovarian development, such as the oxytocin signaling pathway, GnRH signaling pathway, progesterone-mediated oocyte maturation, and AMPK signal pathway. Conclusion The research results enrich the data resources of duck miRNAs, and provide a theoretical basis for further research on the laying performance of poultry and molecular-assisted breeding of poultry in the future.