The Internet Plus Government Services initiative is an important measure to promote the construction of digital government and improve the level of government service. Based on a quasi-natural experiment of the national integrated online government service platform, A-share listed companies in strategic emerging industries from 2008 to 2022 are selected as research samples. The stacked DID model is used to examine the impact and mechanism of government service integration on digital innovation in strategic emerging industries. Research finds that the integration of government services significantly promotes digital innovation in strategic emerging industries. The impact mechanism test finds that the integration of government services mainly promotes digital innovation in strategic emerging industries through channels such as reducing institutional transaction costs, reducing information asymmetry, and improving resource allocation efficiency. The heterogeneity test finds that this promoting effect is mainly reflected in state-owned enterprises, enterprises in the growth and maturity stages, and enterprises with higher internal control quality. Moreover, the stronger the regional innovation capability and the higher the level of technology market development in the place where the enterprise is registered, the better the effect. The research conclusion has enlightening significance for clarifying the micro-governance effects of integrated government services and improving the digital innovation capabilities of strategic emerging industries.