Abstract: Objective To evaluate carriage of Neisseria meningitidis in healthy population in Aksu of Xinjiang, analyze the bacterial community structure and provide references for the control of meningococcal meningitis. Methods Throat swabs were taken from 250 healthy people in 6 age groups selected by stratified cluster random sampling in Aksu. Real-time PCR was performed for serogroup identification of N. meningitides. Results The carriage rate of N. meningitidis in Aksu was 34.40%, serogroup B accounted for 37.21%, serogroup X accounted for 27.91%, serogroup C 17.44%, serogroup Y accounted for 5.81% and the unspecified accounted for 11.63%; the differences in carriage rate among different age group, population and vaccination dose groups were significant. The carriage rate of children aged 6-10 years was 54.39%, higher than those in other age groups. The carriage rates in students and people who had never been vaccinated were high (46.40%, 39.78%). Conclusion The N. meningitidis carriage rate in healthy population in Aksu was high, and the bacterial community structure was complex, and the risk of meningococcal meningitis exists. It is recommend to further strengthen the surveillance for N. meningitidis in healthy population, conduct meningococcal vaccination in susceptible population and take effective measures to control the outbreak of meningococcal meningitis.