In order to investigate the effect of exogenous nitric oxide (NO) on the expression of tomato antioxidant gene under the stress of tomato yellow leaf curl virus (TYLCV), the susceptible tomato Jinpeng 1 was used as the experimental material. Transcriptome sequencing, fluorescent qRT-PCR and bioinformatics analysis were performed under control (CK), TYLCV (TY) and NO+TYLCV (NO+TY) treatments. The results showed that a total of 55 antioxidase-coding genes were selected in the tomato genome, among which the antioxidase-containing genes with the highest number of exons in different subcellular regions were significantly responsive to TYLCV stress. The number of NO-mediated antioxidant enzyme coding genes in different subcellular compartms showed chloroplast>cell membrane>cytoplasm>peroxisome>vacuole, in which the expression levels of Chl Cu-Zn SOD, Chl MR2, Chl GR, Per MR, Pla CAT1 and Pla CAT7 were significantly up-regulated, and the expression levels of Chl Fe SOD1, Chl Fe SOD2, Cyt GPX, Cyt APX1, Cyt APX2 L-5, Pla CAT3, Pla CAT8 and Vac CAT were significantly down-regulated. Fluorescence qRT-PCR verified that Chl GR, Min Mn SOD and Per CAT2 responded to TYLCV, and Chl Cu-Zn SOD, Pla CAT7, Pla CAT8 and Cyt APX2 L-5 responded to TYLCV and NO. Above results provided theoretical basis for studying the mechanism of NO in improving tomato disease resistance.