To study the effect of long-term mining on the microbes in the environment, the soil sampled from Dexing copper ore deposit and its surrounding environment was chosen to be the object of this study. The distribution characteristics of microorganisms in soil were analyzed, and the spatial dependence of between microorganisms and heavy metal elements in surface soil was discussed by using microbial culture method, nucleic acid sequence analysis method and transmission electron microscopy. The experimental results showed that 13 kinds of microbes were isolated from the soil samples in Dawuhe-Gukou riverbank and Zhujiacun. The bacteria isolated from the soil samples in Dawuhe-Gukou riverbank and Zhujiacun had a certain similarity in type and distribution layer; however, to fungi, the similarity between Dawuhe-Gukou riverbank and Zhujiacun was not obvious. The microbial distribution and heavy metal element content in the soil profile had a certain relationship, but not to a simple linear relation, also influenced by various environmental factors.