Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine hesitancy is associated with community aggregation, inducing low vaccine coverage and potentially more frequent community-level outbreak. Addressing vaccine hesitancy in community settings should be a priority for healthcare providers. A cross-sectional online questionnaire survey was conducted during June and July 2022. Ten sites were set up in eastern, central, and western China, from where residents were recruited in a community setting. In total, 7,241 residents from 71 communities were included. Of the residents, 7.0% had refusal administration, 30.4% had delayed administration, and community clustering accounted for 2.4-3.7% and 8.5-9.6% of the variation, respectively. The reasons for primary-dose refusal were diseases, pregnancy, or lactation, whereas the main reasons for booster-dose refusal were diseases during the vaccination period, no time to vaccinate, and felt unnecessary to vaccinate. Younger age (under 40), female, residing in urban settings and having self-reported diseases were sociodemographic indicators of risk for refusal. In the health belief model of refusing to vaccinate, perceived barriers had a positive impact on refusal (β = 0.08), while perceived benefits had a negative impact (β = -0.09). In conclusion, this study underscores the population heterogeneity and community clustering of SARS-CoV-2 vaccine hesitancy. Targeted interventions for these high-risk groups are crucial to enhance vaccination coverage and prevent outbreaks. Public health strategies should address vaccine hesitancy at different stages and doses, while considering both individual beliefs and community dynamics.