Objective To investigate the clinical characteristics, etiology and prognosis of bacterial meningitis in different pathogenic bacteria-infected premature infants and provide evidence for clinical treatment. Methods Clinical data of bacterial meningitis of premature infants hospitalized in the department of neonatology of a children's hospital in Hunan Province from January 2018 to December 2019 were retrospectively analyzed. According to different pathogens of infection, they were divided into Escherichia coli (E. coli) group, other bacteria group and unknown pathogen group. General data, clinical characteristics, cerebrospinal fluid (CSF) examination results and prognosis of three groups of premature infants were compared. Results 90 cases of bacterial meningitis in premature infants were included. The main initial symptoms were poor reaction (58.89%), fever (53.33%), breast refusal (34.44%) and apnea (35.56%), and were the same in early-onset and late-onset bacterial meningitis in premature infants (P>0.05). Among 90 premature infants, 44 were CSF culture positive and were divided into E. coli group (n=18), other bacteria group (n=26) and unknown pathogen group (n=46). The proportion of fever and complications of premature infants in E. coli group and other bacteria group was higher than that in unknown pathogen group (P < 0.05); children whose mothers with premature rupture of membranes and fever before delivery were more likely to suffer from E. coli meningitis (P < 0.05). In E. coli group, inflammation characteristics of CSF bacterial infection of premature infants were more obvious, blood C-reactive protein (CRP) was higher, the appearance of CSF was turbid, with more white blood cell count, higher protein content and lower sugar content (all P < 0.05); prognosis was poorer, the time required for CSF to return to normal and length of hospital stay were longer, incidence of complications was higher (all P < 0.05). Conclusion Clinical manifestations of bacterial meningitis in premature infants are not typical, especially E. coli meningitis, which has a serious disease condition and poor prognosis, it is necessary to be alerted, early diagnosis and treatment should be given.