Innovation serves as the first impetus for high-quality development. The role of government in promoting high-quality innovation development has become a chief driving force. Therefore, based on role theory, this paper will discuss the effect of different government roles on high-quality innovation development and regional alienation, providing policy recommendations for China. In this paper, firstly, a super-efficiency DEA model is introduced to measure the high-quality innovation development level among 30 provinces and municipalities in mainland China from 2010 to 2017. Secondly, a Tobit model is used to analyze the impact of different government roles on high-quality innovation development. The following conclusions are drawn through a super-efficiency DEA model: (1) From the holistic perspective, the high-quality innovation development in mainland China shows a fluctuating growth trend, but its level still needs improvement. (2) From the regional perspective, there is a patchwork pattern of ‘the eastern region ranks highest, followed by the western region and the middle region that stays at the lowest’. In addition, the three regions’ average of total factor productivity of high-quality innovation development has shown a smooth upward trend over the years. Then, the results of Tobit regression analysis are as follows: (1) Apart from the role in supporting talent, roles in constructing innovation platforms, cultivating the innovation environment, and coordinating social resources all pass the significance test. (2) Demands of different government roles vary significantly in different regions from the regional perspective. For the betterment of an innovation society, this paper puts forward suggestions according to different regional development statuses, such as shifting our focus from quantity to quality, strengthening cooperation among provinces and municipalities, and formulating appropriate governance role strategies.