Abstract: Bioactive natural molecules are important resources for the drug development. However, for a long time, no fundamental breakthroughs in the basic theories and investigation methods for research on natural products were achieved. The discovery processes for bioactive natural molecules are still time-consuming, labor-intensive, and unpredictable, which seriously restricted the research efficiency of bioactive natural molecules for innovative drugs development. In recent years, with the rapid development of modern analytical technology, metabonomics, bioinformatics, and artificial intelligence, the research approaches for bioactive natural molecules discovery are revolutionizing, and a number of mass spectrometry (MS)- and nuclear magnetic resonance (NMR)-based dereplication strategies, such as molecular networking (MN) and small molecule accurate recognition technology (SMART), are emerging and applying. This review summarized the MS- and NMR-based novel strategies and methods for efficient discovery of bioactive natural products, aiming to provide some reference for the further development and utilization of these technologies.