Targeting double-stranded DNA (dsDNA) with high affinity and specificity has become a hot topic in biochemistry and molecular biology research. Gene diagnosis and therapy, DNA manipulation, and gene expression regulation could be achieved based on certain recognition principles through specific interactions between dsDNA and natural nucleotides or synthesized ligands. Some ligands (e.g., peptide nucleic acids (PNAs), triple helix-forming oligonucleotides (TFOs), oligopolyamides, and zinc-finger peptides) show sufficient affinity and specificity for targeting dsDNA sequences. PNA can simply synthesize and recognize dsDNA without sequence limitation under physiological conditions. This paper provides a review on the recognition mechanisms, influencing factors, and applications of the four recognition modes of PNA targeting dsDNA. These modes include triplex invasion, triplex binding, duplex invasion, and double duplex invasion. This paper also discusses the challenges to be addressed by future research to fully explore the potential of PNA probe design for specific dsDNA recognition.