Chinese herbal medicines may be contaminated with microorganisms (pathogenic bacteria and mycotoxigenic fungi) during cultivation, harvesting, processing, and storage, which causes spoilage and consequently affects the safety of herbal medicines. This study summarized the microbial contamination of common herbal medicines in recent years, and compared the limits of microbial and mycotoxin in pharmacopeias of different countries. Moreover, we reviewed the detection and identification methods of microorganisms in herbal medicines to provide a reference for similar research.