Aptamers are capable of binding a wide range of biomolecular targets with high affinity and specificity.  It has been widely developed for diagnostic and therapeutic purposes.  Because of unique three dimensional structures and cell-membrane penetration, aptamers inhibit virus infection not only through binding specific target, such as the viral envelope, genomic site, enzyme, or other viral components, but also can be connected to each other or with siRNA jointly achieve antiviral activity.  Taking human immunodeficiency virus and hepatitis C virus as examples, this paper reviewed the effects and mechanisms of aptamers on disturbing viral infection and replication steps.  It may provide an insight to the development of aptamer-based new antiviral drugs.