The innate immune system employs diverse pattern recognition receptors (PRRs) to monitor pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs), thereby initiating innate immune responses against pathogenic invasions. This review focuses on RNA, double-stranded DNA (dsDNA), and non-canonical conformational nucleic acid as structural triggers, comprehensively analyzing the immune recognition mechanisms of nucleic acid-sensing PRRs, their disease relevance, and therapeutic advancements. Key receptors highlighted include Toll-like receptors (TLRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), cyclic GMP-AMP synthase (cGAS), and Z-DNA-binding protein 1 (ZBP1). We elucidate their pivotal roles in antiviral defense, antitumor immunity, and immune homeostasis maintenance, aiming to provide insights for the development of novel PRR-targeted drugs.