Screening analysis that aims at rapidly distinguishing new molecules in the presence of a large number of known compounds becomes increasingly important in the fields of drug metabolite profiling and nature product investigation. In the past decade, online-coupled liquid chromatography-nuclear magnetic resonance spectroscopy-mass spectrometry (LC-NMR-MS) has emerged as a powerful tool for the detection and identification of known and, more important, emerging compounds in complex clinical, pharmaceutical samples and nature product extracts, due to the complementary information provided by the two detectors for unambiguous structure elucidation. This review discusses the practical conditions under which LC-NMR-MS is suitable as a routine tool for unknown analysis, as well as the fundamental concepts and their advantage aspects. Particular attention is paid to its major operating parameters that include the instrumental configurations, working modes, NMR probe improvement and LC mobile phase selection. Finally, the recent applications of LC-NMR-MS to clinical metabolite and nature product analysis are summarized which have shown the benefit of this promising hyphenated technique.