In this paper, we collected water samples and sludge samples respectively along the whole LongJiang River, determined the physical and chemical indexes of all the samples to investigate the water quality and the distribution of heavy metal in LongJiang River. In additional, we applied the modern molecular technology, especially the 16SrRNA high throughput sequencing technology, to investigate the microbial community and research the effects of the distribution of heavy metal on microbial community by analyzing the correlation of the cadmium distribution in LongJiang River and the microbial community.