Objective To investigate the different characteristics of urinary tract microbiome in simple acute or recurrent lower urinary tract infection，and to explore the new directions for the diagnosis and treatment of recurrent urinary tract infection. Methods A total of 53 female patients with simple lower urinary tract infection who were treated in The First Affiliated Hospital of Chongqing Medical University and People’s Hospital of Fengjie from May 2020 to September 2021 were enrolled and divided into acute group with 27 patients and recurrent group with 26 patients. Urine samples were collected for culture，and 16s ribosomal ribonucleic acid next-generation sequencing was used to detect the microbiome in urine. Results At the phylum level，the mean value of OD1 was 0.004 9±0.002 6 in the acute group and 0.002 8±0.001 8 in the recurrent group，and the mean value of Planctomycetota was 0.003 5±0.001 9 in the acute group and 0.002 3±0.002 0 in the recurrent group，with significant differences between the two groups（t=3.444 and 2.160，P=0.001 and 0.035）；at the genus level，as for the genera with a relatively high mean value of relative abundance in the acute group，the mean value of Ochrobactrum was 0.026 9±0.010 9 in the acute group and 0.017 1±0.010 3 in the recurrent group，with a significant difference between the two groups（t=3.372，P=0.001）. There was no significant difference in the median of α diversity between the acute group and the recurrent group，and there was also no significant difference in the median of matrix distance for β diversity between the acute group and the recurrent group［0.277 （0.225，0.361） vs. 0.319（0.240，0.519），F=2.259，R=0.042，P=0.027］；α-Proteobacteria was one of the classification units with a significant difference in median relative abundance between the two groups. Conclusion There are significant differences in the diversity，relative abundance，and dominant flora of the microbiome between the acute group and the recurrent group.