The invention provides a genotyping chip for carrying out joint detection on common viruses in entry-exit inspection and quarantine and a detection method thereof. The genotyping chip for carrying out joint detection on the common viruses in entry-exit inspection and quarantine comprises a solid-phase carrier and an oligonucleotide probe which is fixed on the solid-phase carrier; and the oligonucleotide probe comprises an influenza virus probe, a dengue virus probe, a yellow fever virus probe and a Japanese encephalitis virus probe. In the invention, a method of restrictive fluorescent labeling of virus nucleic acid is adopted to treat nucleic acid to be detected, the probes of influenza virus, dengue virus, yellow fever virus, Japanese encephalitis virus and various viruses are integrated in a multi-virus joint chip of the same chip, various virus nucleic acids can be accurately detected and genotyping can be carried out on an influenza A virus H1N1 subtype, an influenza A virus H3N2 subtype and a dengue virus I-IV type simultaneously.