Soybean mosaic virus (SMV) seriously harms soybean quality and yield. In order to understand the effect of a heterogeneous light environment on the disease resistance of intercropped soybeans, we simulated three kinds of light environments to learn the effects of white light, blue light, and far-red light on the SMV resistance of soybeans. The results showed that compared with the control, SMV-infected soybeans showed dwarfing and enhanced defense. The symptoms of leaves under red and blue light were less severe than those under white light, the virus content of infected plants was about 90% lower than under white light, the activity of antioxidant enzymes increased, and the accumulation of reactive oxygen species decreased. The oxidation damage in SMV-infected soybeans was serious under far-red light. Transcriptome data showed that the biostimulatory response, plant–pathogen interaction, and plant hormone signaling pathway gene expression of SMV-infected soybeans were significantly up-regulated under red light compared with the control. Compared with the control, the genes in the biostimulatory response, calcium ion binding, carbohydrate-binding, mitogen-activated protein kinase (MAPK) signaling, and plant–pathogen interaction pathways, were significantly up-regulated in SMV-infected soybeans under blue light. In far-red light, only 39 genes were differentially expressed in SMV-infected soybeans compared with the control, and most of the genes were down-regulated. Compared with the control, the up-regulation of the salicylic acid (SA) pathway defense gene in SMV-infected soybeans under red light was higher than under other light treatments. Compared with the control, the up-regulation of the jasmonic acid (JA) and ethylene (ET) pathway defense genes in SMV-infected soybeans under blue light was higher than under other light treatments. Compared with the control, most defense-related genes in the SA and JA pathways were inhibited in SMV-infected soybeans under far-red light, while genes in the ET pathway were significantly up-regulated. These results will advance our understanding of the disease resistance mechanism of intercropping soybeans in a heterogeneous light environment and provide new ideas for the prevention and control of viral diseases.