Abstract: 【Objective】 To screen miRNA and target genes in response to NaCl stress in Malus sieversii. 【Methods】 In this study, tissue culture seedlings of Malus sieversii were used as experimental materials and small RNA sequencing was performed on leaves of Malus sieversii seedlings treated with 150 mmol/L NaCl for 6 h and 48 h. 【Results】 The results showed that: compared with the control group, 3 miRNAs were differentially expressed when NaCl treatment lasted for 6 h, among which 2 were up-regulated and 1 was down-regulated, and the corresponding target genes of miRNA were 64. When NaCl treatment lasted for 48 h, 13 miRNAs were differentially expressed, among which 4 were up-regulated, 9 were down-regulated, and the corresponding target genes of miRNA were 108. The differential target genes were classified and annotated by GO and KEGG. When NaCl treatment lasted for 6 h, GO enrichment mainly included: inositol pentakisphosphate 2-kinase activity, oligosaccharyl transferase activity, tRNA wobble adenosine to inosine editing, xylan biosynthetic process, etc. When NaCl treatment lasted for 48 h, GO enrichment mainly included: oxidoreductase activity, DNA binding, Apoplast, secondary metabolic process, etc. KEGG co-accumulate in the N-glycan biosynthesis pathway. 【Conclusion】 qRT-PCR verified that the expression levels of mdm-mir168b, mdm-mir159c, mdm-mir827, mdm-mir390f, mdm-mir171i and mdm-mir399j were different when NaCl treatment lasted for 6 h and 48 h, and the expression levels of mdm-mir390f and its target genes HF10976, mdm-mir171i and its target genes HF33844, mdm-mir399j and its target genes HF11095 were negatively correlated. These three miRANs were involved in the response process of Malus sieversii to NaCl stress.