China has made remarkable achievements in the construction of the National Innovation System (NIS), but the theoretical and empirical studies on the NIS's overall effectiveness have lagged behind the policy and management practice. From the perspective of system theory, this study defines the concept of NIS's overall effectiveness, and constructs a comprehensive evaluation system of NIS's overall effectiveness based on the panel data of China (mainland) from 2012 to 2020, using a combination assignment method and coupled coordination model for measurement and analysis. We also conducted a configuration analysis of the factors influencing the NIS's overall effectiveness using a fuzzy set qualitative comparative analysis approach (fsQCA). The results show that: First, from a temporal perspective, China's NIS's overall effectiveness has grown by leaps and bounds, with a 326.77% increase in 2020 compared to 2012. Second, from a spatial perspective, the top five regions in terms of the NIS's overall effectiveness from 2012 to 2020 are Guangdong Province, Jiangsu Province, Beijing, Shanghai, and Zhejiang Province, while the bottom five regions are Yunnan Province, Ningxia Province, Guizhou Province, Gansu Province, and Qinghai Province. The spatial distribution pattern of the NIS's overall effectiveness is "East > Central > West". Third, the factors driving the NIS's overall effectiveness are in three Configurations. The first type is a two-wheel drive of government innovation support and infrastructure construction, a typical case is Jiangsu Province. The second type is the two-wheeled government innovation support and digital economy, a typical case is Zhejiang Province. The third type is the three-legged government-infrastructure-digital economy support type, a typical case is Guangdong Province.
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