Objective To study the clustering of Streptococcus pneumoniae carriage among school children aged 6-10 years in Haidong City of Qinghai Province, and its influencing factors, providing scientific evidence for preventing and controlling the transmission of Streptococcus pneumoniae in this population. Methods Multistage stratified cluster sampling and simple random sampling were used to select 834 healthy children aged 6-10 years from seven kindergartens and five primary schools in Haidong City of Qinghai Province. Oral and nasal swabs were collected for isolation and identification of Streptococcus pneumoniae. Parents completed questionnaire surveys. Data analysis was performed using chi-square tests and random-effects logistic regression models. Results The carriage rate of Streptococcus pneumoniae was 21.6% (180/834). Cluster analysis showed statistically significant random effects at the school level (Z=2.965, P=0.003; ICC=14.189%). Children aged 8-10 years had a lower carriage rate than those aged 6-7 years (OR=0.467, 95%CI: 0.232-0.938, P=0.032). Children living in households with more than three cohabiting individuals had a higher risk of carriage compared to those with three or fewer (OR=1.541, 95%CI: 1.016-2.339, P=0.042). Conclusions Streptococcus pneumoniae carriage among school children aged 6-10 years in Haidong City of Qinghai Province exhibits school-level clustering. Age and number of cohabiting individuals are significant influencing factors for carriage.