Over the past ten years, the number of three-dimensional protein structures identified by advanced science and technology increases, and the gene information becomes more available than ever before as well. The development of computing science becomes another driving force which makes it possible to use computational methods effectively in various phases of the drug design and research. Now Structure-Based Drug Design (SBDD) tools are widely used to help researchers to predict the position of small molecules within a three-dimensional representation of the protein structure and estimate the affinity of ligands to target protein with considerable accuracy and efficiency. They also accelerate discovery speed of potent drug and reduce the cost and times for drug research. Here we present an overview of SBDD used in drug discovery and highlight its recent successes and major challenges to current SBDD methodologies.