Integrating into the global innovation system is the only way for local manufacturing companies to innovate their strategies. Breaking through the paradigm limitation of Global Value Chain research, this paper is based on the new paradigm of Global Innovation Chain, from the perspective of “heterogeneity” hypothesis and binary relationship, revealing the heterogeneous Global Innovation Chain governance of “deconstruction type, division of labor and spatial structure” under different contexts such as “technical paradigm, technology gap and power status”, significant differences in the technical capacity spillover (“fish” effect) and innovation capacity spillover (“fishing”effect) of local manufacturing companies. The multi-value Qualitative Comparative Analysis (mvQCA) method is used to analyze the complex path configuration of 80 heterogeneous Global Innovation Chain governance binary relations samples, revealing the heterogeneity dimension and situational characteristics of global innovation chain governance, and the interaction and matching mechanism of the “fish/fishing” effect. The conclusions of the study are instructive for exploring the new paradigm of Global Innovation Chain research and the strategic decision of local manufacturing enterprises for the integration into the Global Innovation Chain.