Soil salinization has become an important factor limiting crop yield and quality, affecting crop yields worldwide. As an important fruit crop, the harm of salt stress and the lack of salt tolerant rootstocks have become important issues threatening the healthy and sustainable development of the modern apple industry. Therefore, studying the response and adaptation of apple trees to salt stress is of great practical significance and urgency. In this study, total RNA was extracted from the leaves and roots of Malus zumi (Mats.) Rehd. seedlings were treated with 0, 0.2% and 0.6% NaCl after 0, 4, 8 and 12 days, and RNA-seq libraries were constructed. A total of 575 miRNAs were identified, including 315 known mdm-miRNAs and 260 new miRNAs. In addition, differentially expressed (DE) miRNAs exhibited tissue-specific expression patterns in response to salt stress. At the same time, a data set for deep sequencing of miRNA in Malus zumi (Mats.) Rehd was provided, and bioinformatics methods were used to control the quality of the original data. High quality sequences were obtained, and BLAST software was used to compare the predicted target gene sequences with NR, Swiss Prot, Pfam and other databases to obtain annotation information of salt tolerance related genes. GO analysis shows that miRNAs and target genes related to salt stress are mainly involved in the response to stimuli in biological processes. This will provide theoretical data basis for the utilization of Malus zumi (Mats.) Rehd and favorable support for the breeding of salt tolerant rootstocks.