As an important aspect of bioinformatics, the main problem of Genome Sequencing is DNA Fragment Assembly. This paper proposed a new fragment assembly algorithm based on the long fragment filtration. Firstly, the fragment set was divided into two parts according to a threshold of the filtration length and the Bruijn graph was formed by the short fragments set. Subsequently system automatically selected long fragments which met the filtration condition by the Bruijn graph and the path searching method and constructed the filtrated fragments set. On the basis of not missing essential fragment information in the process of fragment assembly, our method effectively resolved the problem of high spatial cost and limited processing scale caused by traditional Eulerian Super path method. Finally, we certified the feasibility and the validity of our method through a series of experiments.