Objective To obtain higher microbiological quality of Mongolian gerbil colonies and realization of experimental animalization by biological cleaning. Methods We conducted biological cleaning of Mongolian gerbils by selection of pregnant gerbils, perinatal judgment, aseptic Caesarean section, pup milk replacer and breeding in individually ventilated cages. We also compared the results by milk replacer for pup gerbils from lactating ICR mice, rats as well as gerbils. Results During the present study, 85 Caesarean operations were carried out and a total of 167 gerbils were weaned. Conclusions We have successfully achieved the biological cleaning from a Mongolian gerbil colony in Zhejiang province, and the key techniques may provide useful reference for biological cleaning of special laboratory animal species in China.