The sialic acid (SA)-phenylboronic acid (PBA) recognition system is of particular interest in the bioconjugation field, because it is simple, fast, efficient, and biocompatible. In this paper, we report a novel method for reversibly labeling living virus with quantum dots (QDs) by taking advantage of this SA-PBA recognition system. The QDs were initially modified with PBA (QDs-PBA) to target them to the surface of vesicular stomatitis virus (VSV), which has abundant with SA on its envelope. The QDs-PBA was of good monodispersity and strong fluorescence, and could be conjugated with VSV by simply incubating with native VSV for 10 min at 37 °C, producing QDs-VSV that was capable of being imaged at the single virion level. The labeling efficiency attained 83 ± 4.3 % (mean ± SD); meanwhile, the activity and recognition ability of the labeled virus were minimally affected. This method was simple, rapid, and reversible. This work promotes the virus labeling development to a new step. That is, native viruses can be reversibly labeled without any modification.