Abstract: Based on a method of miniature animal diversity survey in polluted water and PFU indoor toxicity test, demonstrates a comparative study about the pollution effect of production wastewater in microfauna community level from a Fermenting Pharmaceutical company. The statistical analysis shows, there is a remarkably reducing effect in miniature aquatic biodiversity according to the current emission standard discharge. Using this effect, the environmental risks of fermenting pharmaceutical wastewater can be monitored and warmed early.