Objective To study the clinical significance of the microorganism culture result of amniotic fluid in cesarean section in the treatment of anti-infection after operation. Methods From August 2016 to May 2017 in Women’s and Children’s Hospital of Sichuan Province, 502 amniotic fluid samples were collected in cesarean section to carry out bacteria culture. The correlations between the amniotic fluid culture result and the preoperative and intraoperative risk factors and the correlations between postoperative infection and the preoperative and intraoperative risk factors were analyzed. Results In the 502 amniotic fluid samples, there were 131 samples culture-positive. The microbiological culture results of amniotic fluid were statistically different between the puerperae with gestational age<37 weeks and the ones with gestational age≥37 weeks (P=0.001). Postoperative infection occurred in 6 puerperae, in whom the amniotic fluid culture results were positive in 3 puerperae. There was no statistical difference in the occurrence of postoperative infection between the puerperae with amniotic fluid culture-positive results and the ones with negative results (P=0.382). The occurrence of postoperative infection was associated with preoperative infections, gestational age, using time of antimicrobial, and preoperative rupture of membranes (P<0.05). Conclusions The contamination rate of amniotic fluid specimen was high, which was of low reference value to anti-infection treatment after operation. When an extension of anti-infection treatment be carried out after cesarean section, suitable specimens should be selected according to the infection site.