Abstract: OBJECTIVE To compare pharmaceutical water microbiological testing methods of national pharmacopoeia and explore rationalities of various methods. METHODS The water system of five pharmaceutical companies in Zhejiang province were tested with Chinese Pharmacopoeia, European Pharmacopoeia and United States Pharmacopoeia methods on the basis of analysis and comparison of their similarities and differences. RESULTS There were significant differences in the detection efficiency of pharmaceutical water pollution bacteria among domestic and international pharmacopoeia, especially for slow-growing oligonucleotide bacteria. CONCLUSION European Pharmacopoeia methods are conducive to recycling of contaminated bacteria in the water system, especially oligotrophic and slow-growing bacteria.