Green innovation is deemed as a sound solution to balance socioeconomic development and eco-environmental improvement. The driving force of green innovation have received increasing attention from scholars. However, research on the driving effect of regional integration development on green innovation remains scant. To bridge the research gap, based on the panel data of China's main urban agglomerations from the year of 2006–2017, we constructed an index system to evaluate urban green innovation comprehensive level and applied baseline regression model and spatial econometric model to detect how regional integration development affects green innovation. The main findings are as follows: (1) The average green innovation level in China's major urban agglomerations harbors an upward trend when it increases from 0.11 to 0.47, although there is an uneven development pattern when the urban agglomeration with the highest green innovation level (0.62) from eastern region and the lowest one (0.34) from western region. (2) Empirical results show that improving regional integration level can significantly drive the green innovation development through some effective paths such as the advancement of foreign direct investment, financial development, and economic agglomeration. (3) Regional integration development exerts the pronounced spatial spillover effect on green innovation and promotes the green innovation level of local and adjacent cities. Thus, the research findings would provide new insights into the relationship and interaction between regional integration development and green innovation when exploring and seeking the multiregional sustainable development path from a story of China.