Globally, the rollout of COVID‐19 vaccine had been faced with a significant barrier in the form of vaccine hesitancy. This study adopts a multi‐stage perspective to explore the prevalence and determinants of COVID‐19 vaccine hesitancy, focusing on their dynamic evolutionary features. Guided by the integrated framework of the 3Cs model (complacency, confidence, and convenience) and the EAH model (environmental, agent, and host), this study conducted three repeated national cross‐sectional surveys. These surveys carried out from July 2021 to February 2023 across mainland China, targeted individuals aged 18 and older. They were strategically timed to coincide with three critical vaccination phases: universal coverage (stage 1), partial coverage (stage 2), and key population coverage (stage 3). From 2021 to 2023, the surveys examined sample sizes of 29 925, 6659, and 5407, respectively. The COVID‐19 vaccine hesitation rates increased from 8.39% in 2021 to 29.72% in 2023. Urban residency, chronic condition, and low trust in vaccine developer contributed to significant COVID‐19 vaccine hesitancy across the pandemic. Negative correlations between the intensity of vaccination policies and vaccine hesitancy, and positive correlations between vaccine hesitancy and long COVID, were confirmed. This study provides insights for designing future effective vaccination programs for emerging vaccine‐preventable infectious X diseases.