A new parallel processing approach for ClustalW was presented and described in this paper. This approach uses Desktop Grid Computing Platform, which is a promising idea for high performance computing as its programming environment and running platform. On Desktop Grid computing platform, task partition, parallelism strategy and implementation technology of clustalW algorithm program were discussed in detail. ParaClustalW policy is load balances which was strongly supported for its consideration of alignment length and number factors. In order to demonstrate the effectiveness of this approach, a serial of simulation experiments were also done. The results obtained from performance analysis show that it gained a quick working time and good speedup. Under the same machine configuration, our approach is better than other solutions and it is a feasible and valuable approach for Multiple Sequence Alignment in bioinformatics.