Research indicates that integration contributes to maintaining health among migrants, yet little is known about the association between integration and vaccination acceptance. This study aimed to explore COVID-19 vaccine intention and acceptance, and the association between integration and vaccine hesitancy among migrants in Japan. We conducted an internet survey among migrants in Japan from October 5 to October 14, 2021. Among 1,455 participants, 11.6% reported hesitancy toward COVID-19 vaccination. We found that the overall integration and social integration were associated with the vaccination intention. Some commonly identified barriers (e.g., financial difficulties, language) were not related to COVID-19 vaccination acceptance among migrants in Japan. Highly integrated migrants were less likely to report vaccine hesitancy against COVID-19. To promote COVID-19 acceptance among migrants, customized intervention policies should focus on the migrants with a lower level of integration, especially those with little social connection with the locals.