Nonsense-mediated mRNA decay (NMD) removes aberrant transcripts to avoid the accumulation of truncated proteins. NMD regulates nucleotide-binding, leucine-rich repeat (NLR) genes to prevent autoimmunity; however, the function of a large number of NLRs still remains poorly understood. Here, we show that three NLR genes (, , and ) are important for NMD-mediated regulation of defense signaling at lower temperatures. At 16 °C, the NMD-compromised () mutants showed growth arrest that can be rescued by the artificial miRNA-mediated knockdown of the three NLR genes. mRNA levels of these NLRs are induced by inoculation and exogenous SA treatment. Mutations in , , and genes resulted in increased susceptibility to , whereas their overexpression resulted in severely stunted growth, which was dependent on basal disease resistance genes. The NMD-deficient mutants accumulated higher levels of NMD signature-containing transcripts from these NLR genes at 16 °C. Furthermore, mRNA degradation kinetics showed that these NMD signature-containing transcripts were more stable in mutants. Based on these findings, we propose that , , and are directly regulated by NMD in a temperature-dependent manner and play an important role in modulating plant immunity at lower temperatures.