Molecular docking technology is an effective approach to protein-ligand interactions and recognition. The near-native conformations generated in the interaction process are the lowest energy conformations, so it is pivotal for the protein-ligand docking to searching these conformations quickly and accurately. Here we reviewed the main conformational searching methods in protein-ligand docking, including the exhaustive searching, heuristic searching and other searching strategies. Meanwhile, we listed the representative docking programs by using these different searching strategies. Furthermore, we introduced the international assessment of predicted interaction, the widely used testing benchmark and the evaluation indexes in protein-ligand docking. Finally, we pointed out the existing major problems of the search strategies in protein-ligand docking and gave a prospect for such field in the near future.