Abstract: To study the mechanism for treating tobacco mosaic virus (TMV) with compound sodium chlorite (500 mg/L), the expression levels of the virus CP gene and rep gene were detected by fluorescence quantitative RT-PCR, and the damage degree of TMV CP was determined by indirect enzyme-linked immunosorbent assay. After inoculating TMV to Nicotiana glutinosa, the infection activity of TMV was analyzed by counting the number of withered spots. The damages of corresponding TMV gene fragments were detected by large fragment step-by-step RT-PCR, and the destruction of virus particles was observed by transmission electron microscope. The results showed that: 1) The expression of TMV CP gene was completely inhibited by the 30-min drug treatment and the expression of TMV rep gene was completely inhibited by the 60-min drug treatment. After the treatment, TMV CP was completely destroyed, and the virus also completely lost its ability to infect the host Nicotiana glutinosa. 2) After the 30-min drug treatment, 183kDa-2, 183kDa-4 and coding regions of CP & MP among six regions (183kDa-1, 183kDa-2, 183kDa-3, 183kDa-4, 54kDa and the coding regions of CP & MP genes) of TMV were damaged first, but the amplifications of the three regions in leaf vein and petiole of inoculated tobacco were normal. After treating for 45 min, the amplifications of the 183kDa-1, 183kDa-3 and 54kDa regions of leaf veins, petioles and upper leaves were normal, while those of the other three gene regions were not. The amplifications of the six gene regions of the control leaf, stem and lower leaf of inoculated tobacco were abnormal. After treating for 60 min, the amplifications of all the regions were negative. Therefore, it could be determined that CP damage caused by the drug treatment was the main factor leading to the disappearance of virus infectivity, and nucleic acid damage was not related to virus inactivation. 3) Transmission electron microscopy indicated that the virus particles were completely broken into fragments after 1.5 h drug treatment.