Interactions between proteins and ligands are ubiquitous and indispensable in the process of life. These interactions play important roles in the biological molecular recognition and in the process of signal transmission. Identifying the binding residues of the protein-ligand interactions has important scientific significance for protein function research, drug design and screening. Biocomputing method has become an important method for the prediction of protein-ligand binding residues. This paper first describes the common definition of the binding residues of the protein-ligand interactions. Next, a systematic category of protein-ligand binding residue prediction is proposed, and several prediction methods in each category are described. This paper then demonstrates the related protein databases and the evaluation indexes, and experimentally compares and analyzes the performances of some representative prediction methods on the corresponding data sets. Finally, the future research directions of protein-ligand binding residue prediction are proposed, which provide some references for relevant researchers engaged in the field of protein-ligand binding residue prediction.