Long non-coding RNAs (lncRNAs) are important in regulating the response to environmental stresses in organisms. In this study, we used Caenorhabditis elegans as an animal model to determine the functions of intestinal lncRNAs in regulating response to simulated microgravity stress. Among the intestinal lncRNAs,
linc-2,
linc-46,
linc-61, and
linc-78 were increased by simulated microgravity treatment, and
linc-13,
linc-14,
linc-50, and
linc-125 were decreased by simulated microgravity treatment. Among these 8 intestinal lncRNAs, RNAi knockdown of
linc-2 or
linc-61 induced a susceptibility to toxicity of simulated microgravity, whereas RNAi knockdown of
linc-13,
linc-14, or
linc-50 induced a resistance to toxicity of simulated microgravity. In simulated microgravity treated nematodes,
linc-50 potentially binds to three transcriptional factors (DAF-16, SKN-1, and HLH-30). RNAi knockdown of
daf-16,
skn-1, or
hlh-30 could suppress resistance of
linc-50(RNAi) nematodes to the toxicity of simulated microgravity. Therefore, our results provide an important basis for intestinal lncRNAs, such as the
linc-50, in regulating the response to simulated microgravity in nematodes.