Convolution computing plays an important role in scientific computing. There exist massive message passing, load-unbalancing in traditional MPI model. Concerning this question, a new parallel convolution based on MPI model was proposed in this paper. This model prevents massive message passing, and keeps load-balancing. By analyzing the speedup ratio and efficiency, the experimental result shows that the new MPI parallel programming obviously promotes parallel efficiency and large-scale sequence’s speed, which exerts the advantages of distributional memory between nodes and parallel computing. It is an effective and feasible parallel strategy.