Enriched the drinking water by using tangential flow ultrafiltration (TFF), extracted the genomic DNA, amplified 16S rDNA V4+V5 region, a total of 45 093 sequences and the average length of the 395.65 bp sequence were got. After high throughput sequencing bioinformatics analysis including annotation, evaluation, species composition analysis, β- diversity analysis, species difference analysis, RDA analysis etc., the bacterial diversity and the abundance in drinking water was got. In the result, the bacterial diversity is uncertainty and randomness in drinking water, the water quality parameters of turbidity and residual chlorine are biggest influence on the bacterial diversity in drinking water, but the bacteria bio-information which got by Illumina MiSeq high-throughput sequencing may exist without activity or ‘viable but non-culturable bacteria’, but these bacteria are difficult to culture. High-throughput sequencing technology is a good technology for analyzing the bacteria in drinking water.