Coptis chinensis is widely used as Chinese medicine herbs and serious soil problems occur after continual cultivation of this medicinal plant. In the preset experiment, fibrous root extract of C. chinensis (REC) was added into soil to study the effect of REC on microbes and enzyme activity in soil. The results showed that both bacteria and actinomycetes decreased by about 2 times in contrast to fungi, which increased by about 3 folds. Phosphorus bacteria, potassium bacteria, azotobacter, ammonia bacteria, and nitrifying bacteria were also reduced significantly by REC, suggesting the inhibition of nitrogen biofixation and supply, mobilization of phosphorus and potassium, ad plant growth promotion as REC added into soil. There were multiple influences of REC on soil enzyme activities. Invertase activity was stimulated, while urease was inhibited and dehydrogenase unchanged by REC, indicating the interference of biochemical reactions in soil. In addition, type and total content of phosphorus lipid fatty acids (PLFAs) , the signature of microbes, decreased while the ratio of bacterium to fungus PLFAs increased as REC increased in soil, which suggested that fungi increased relatively with bacteria decreased thereby leading to easy occurrence of crop fungus diseases following cultivation of C. chinensis. The decrease in diversity and evenness indexes of microbial community in soil by REC indicated soil ecosystem deterioration and reduction of microbial groups and densities in soil. Therefore, allelopathic chemicals released from the roots of C. chinensis could change microbial community structure and resulted in serious soil problems by continual cropping of this medicinal plant.