Extraction of metagenomic DNA from environmental sample was the main restrictive factor for the metagenomic sequencing. Three different extraction methods were used and compared in this study. The results indicated that the metagenomic DNA obtained from the activated sludge by Liquid Nitrogen Grinding+DNA Extraction Kit was the best sample due to the largest information and best quality, and D（260／280 nm） was between 169-172. During the sample preparation for the next generation sequencing, D（260／280 nm） of the metagenomic DNA reached to 183 after purification, which met the requirement of library construction. After the sequencing by Solexa Genome Analyzer System, the results showed that the forward sequencing of these two samples was successful, and the high quality data was about 908％, which could be used for assemble.