Abstract: Natural products are valuable resources for discovering new drugs. So far, screening bioactive compounds from organism extracts is still an important and challenging task. Traditional biometric guided method involves repeated fractionation steps and bioactivity tests, which are time-consuming, labor-consuming, and inefficient. Ligand fishing is a bioanalysis method for screening ligands from complex organism extracts based on intermolecular affinity interactions. It has the characteristics of strong specificity, high efficiency, and less requirement for sample pretreatment. In this review, we summarize the classification of ligand fishing strategy and its application in enzyme inhibitors screening. Finally, the development prospects of this technology are forecasted.