Abstract：Objective：High-throughput sequencing analysis was performed in adult islets of normal mice and intrauterine growth retardation (IUGR) mice during pregnancy, which screened out differentially expressed long noncoding RNA (lncRNA) and messenger RNA (mRNA) to provide a theoretical basis for further exploring the pathogenesis of islet dysfunction in pregnant mice born with IUGR. Methods: Islets were extracted from IUGR and normal pregnant mice for high-throughput sequencing analysis. The differentially expressed lncRNAs and mRNAs were screened out?and association analysis between them was performed. We conducted gene ontology (GO) analyisis, Kyoto Encyclopedia of gene and genome (KEGG) enrichment analysis on taget mRNAs of differentially expressed lncRNAs. Emphasis was placed on the highly differentially expressed lncRNAs, especially those that may be involved in the regulation of islet function during pregnancy. Results: There were 1007 differentially expressed lncRNAs between IUGR pregnancy (IP) and normal pregnancy (NP) , among which 483 were up-regulated and 524 were down-regulated. 50 mRNAs were differentially expressed, of which 22 were up-regulated and 28 were down-regulated. The GO analysis of differentially expressed lncRNAs’target mRNAs and differentially expressed mRNAs showed that biological process (BP) mainly focused on cellular and tissue processes, biological regulation, metabolism and stress processes; Molecular functions (MF) were concentrated in integration, catalytic activity, transport activity, molecular function regulation,etc. KEGG enrichment analysis highlighted the involvement of metabolic pathway, cancer pathway, biosynthesis of secondary metabolites, PI3K-AKT pathway and MAPK pathway. We furether analysed lncRNA FTX and Neat1. The expression level of FTX in normal mice and IUGR mice during pregnancy decreased (P＜0.001), while LncRNA Neat1 increased (P＜0.01). FTX and Neat1 exhibited significantly difference in the expression between IP and NP (P＜0.05), and both were regulated by glucose concentration. The association between lncRNA FTX and its target mRNAs was trans action. The association between lncRNA Neat1 and Frmd8 was cis action, while the rest were trans action. Conclusions: In this study, differentially expressed lncRNAs and mRNAs in adult islets of normal mice and intrauterine growth retardation (IUGR) mice during pregnancy were screened. Besides, lncRNAs can regulate target mRNAs through different interaction modes, thus influencing glucose metabolism, which provides new ideas for further exploring the pathogenesis of islet dysfunction in pregnant mice born with IUGR.