Objective Long non-coding RNA (LncRNA) plays a significant role in regulating feed efficiency. This study aims to explore the key lncRNAs, associated genes, and pathways in pigs with extreme feed efficiencies. Methods We screened pigs with extremely high and low residual feed intake through a 12-week animal growth trial and then conducted transcriptome analysis on their liver and ileum tissues. We analyzed the differential expressed lncRNAs, microRNAs (miRNAs), and messenger RNAs through target gene prediction and functional analysis. And we identified key lncRNAs and their potential regulatory genes associated with feed efficiency through the construction of competitive endogenous RNA network. Results Differentially expressed lncRNAs were pinpointed in the liver, revealing 23 crucial target genes primarily associated with guanosine triphosphate metabolism and glycolipid biosynthesis. In the ileum, a screening identified 92 pivotal target genes, mainly linked to lipid and small molecule metabolism. Moreover, LOC106504303 and LOC102160805 emerged as potentially significant lncRNAs respectively, playing roles in mitochondrial oxidative phosphorylation in the liver, and lipid and cholesterol metabolism in the ileum. Conclusion The lncRNAs regulate energy metabolism and biosynthesis in the liver, and the digestive absorption capacity in the small intestine, affecting the feed efficiency of pigs.