In the last ten years, high-performance and massively parallel computing technology comes into a high speed developingphase and is used in all fields. The cluster computer systems are also being widely used for their low cost and high performance. Inbioinformatics research, solving a problem with computer usually takes hours even days. To speed up research, high-performancecluster computers are considered to be a good platform. Moving into the new MPP (massively parallel processing) system, the originalalgorithm should be parallelized in a proper way. In this paper, a new parallelizing method of useful sequence alignment algorithm(Smith-Waterman) is designed based on its optimizing algorithm already exists. The result is gratifying.