How market integration promoted by local government coordination affects the cross-regional innovative cooperation of micro-enterprises is an issue that has not yet been verified. Based on the interregional market integration led by the Coordination Committee for the Urban Economy of the Yangtze River Delta ( CCUE-YRD) and patent joint research and development data for enterprises in different cities, this paper explores how government coordination affects the overall preference characteristics and innovative performance of enterprises in the selection behaviour of cooperative innovative partners among the integrated cities. The innovative cooperation effect between CCUE-YRD member cities is found to have improved significantly, while that of single-member cities has decreased significantly. The reason for this is that the market integration effect of the CCUE-YRD promotes the spatial functional division of labour among cities and the structural differentiation of industrial knowledge innovation, and it relies more on interregionaltrust. This paper also finds that the economic effect of innovation cooperation varies based on the theme of conferences and high-speed railway connection, and there is a bias towards state-owned enterprises.