Virus-induced gene silencing (VIGS) is a natural defense mechanism of plants, which can cause sequence-specific degradation of viral RNA and is often used for studying the functional genome. At present, the VIGS system mediated by Tobacco rattle virus (TRV) has been successfully established in many plant species. However, the VIGS system in Chinese narcissus had not been reported yet. In this paper, the first use of the TRV-VIGS system in Chinese narcissus is described in detail. By injecting pTRV2-GFP into narcissus leaves, we confirmed that TRV could infect narcissus and move in narcissus plants. After the inoculation of pTRV2-NtPDS by two methods, phenomena such as photo-bleaching appeared in narcissus leaves and qRT-PCR results proved that PDS gene of narcissus was successfully silenced. Besides, pTRV2-NtMYB3 was inoculated into basal plates of narcissus to study the function of NtMYB3; the results showed that NtMYB3 is an inhibitor of flavonoids biosynthesis, which can increase the content of proanthocyanidins in basal plates of narcissus by repressing the expression level of NtFLS. These results indicate that the TRV-VIGS system has been successfully established in Chinese narcissus and successfully applied to the functional study of NtMYB3.