Therapeutic oligonucleotides (ONs), including antisense-oligonucleotides, small interfering RNA, aptamers, and conjugated modalities, have emerged as an important class of drugs with increasing clinical impact. Unlike small molecules, ONs undergo metabolism primarily through nuclease-mediated cleavage, generating complex profiles of shortened metabolites that often differ by a single nucleotide and may retain pharmacological or toxicological relevance. Comprehensive metabolite identification is therefore essential for understanding ONs pharmacokinetics (PK), tissue exposure, and safety. Liquid chromatography coupled to mass spectrometry (LC-MS) has become the principal analytical platform for ONs metabolite identification. Recent advances in chromatographic separation, high-resolution mass spectrometry, fragmentation strategies, and data processing tools have substantially improved the depth, confidence, and throughput of metabolite characterization. This review provides an overview of ONs biotransformation pathways and critically examines modern LC-MS strategies used for metabolite separation, detection, and structural elucidation. Emphasis is placed on high-resolution MS acquisition approaches, charge-state management, complementary fragmentation techniques, and software-assisted metabolite annotation. Emerging trends and future directions in ONs metabolite analysis are also discussed, with a focus on supporting translational PK and regulatory decision making.