Soybean (Glycine max) is a major oil and feed crop worldwide. Soybean mosaic virus (SMV) is a globally occurring disease that severely reduces the yield and quality of soybean. Here, we characterized the role of the clock gene TIMING OF CAB EXPRESSION 1b (GmTOC1b) in the resistance of soybean to SMV. Homozygous Gmtoc1b mutants exhibited increased tolerance to SMV strain SC3 due to the activation of programmed cell death triggered by a hypersensitive response. Transcriptome deep sequencing and RT-qPCR analysis suggested that GmTOC1b likely regulates the expression of target genes involved in the salicylic acid (SA) signaling pathway. GmTOC1b binds to the promoter of GmWRKY40, which encodes a protein that activates the expression of SA-mediated defense-related genes. Moreover, we revealed that the GmTOC1b^H1 haplotype, which confers increased tolerance to SMV, was artificially selected in improved cultivars from the Northern and Huang-Huai regions of China. Our results therefore identify a previously unknown SMV resistance component that could be deployed in the molecular breeding of soybean to enhance SMV resistance.