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Achieving safe and efficient gene therapy hinges upon the inspection of genomes enclosed within individual nano‐carriers to mitigate potential health risks associated with empty or fragment‐filled vectors. Here solid‐state nanopore sensing is reported for identifications of intermediate adeno‐associated virus (AAV) vectors in liquid. The method exploits the phenomenon of translocation slowdown induced by the viscosity of salt water‐organic mixtures. This enables real‐time ionic current measurements allowing precise tracking of the electroosmotic flow‐driven motions of recombinant AAV vectors in a nanopore. The resulting ionic signals facilitate discrimination between replicative intermediates carrying ssDNA fragments and its full vector counterparts based on genome length‐derived subtle nanometer differences in the viral diameters. This rapid and non‐destructive means of genome analysis within virus capsids provides a promising avenue toward a robust methodology for ensuring the integrity of AAV vectors before administration. [ABSTRACT FROM AUTHOR]