At present, the COVID-19 pandemic is still ongoing globally and the virus is constantly mutating. The herd immunity barrier established by past infections or vaccinations is gradually weakening and reinfections are occurring. To evaluate the pandemic fatigue and vaccine hesitancy among people who have recovered from COVID-19 in the post-pandemic era, we conducted an anonymous cross-sectional survey study in China from 4 July to 11 August 2023, nearly 6 months after the last large-scale nationwide infection. Basic sociodemographic characteristics, health-related factors (smoking, drinking, and chronic disease history), COVID-19 vaccination history, and self-reported long COVID were obtained as potential covariates. A series of logistic regression models were performed to examine the association between pandemic fatigue and vaccine hesitancy toward the next dose of COVID-19 vaccines via crude relative risks (cORs) and adjusted relative risks (aORs) with 95% CIs. According to our results, of the 2942 participants, 1242 (42.2%) were hesitant (unwilling or not sure) to receive the next dose of COVID-19 vaccines. The average score on the Pandemic Fatigue Scale was 21.67 ± 8.86, in which the scores of all items in the vaccine-hesitant group were significantly higher than those in the vaccine-accepting group. Additionally, the higher the pandemic fatigue level among people who have recovered from COVID-19, the more likely they were to be hesitant to receive the next dose of the COVID-19 vaccines (moderate: aOR = 2.94, 95% CI: 2.46–3.53; high: aOR = 6.88, 95% CI: 5.49–8.64). Overall, more than 40% of the recovered participants were unwilling or uncertain about the next vaccine dose, with varying degrees of pandemic fatigue. Pandemic fatigue is a potentially relevant factor for vaccine hesitancy and may hinder the translation of vaccination intention into behavior. Considering the ongoing reinfection situation, implementing a health education plan to reduce pandemic fatigue and prioritizing vaccination issues for people who have recovered from COVID-19 may be key to promoting the reduction of the COVID-19 disease burden and ensuring the health and well-being of the population.