Based on a comprehensive sample of Chinese A-share listed new energy vehicle companies from 2011 to 2023, this study employs a multi-methodological approach integrating theoretical modeling, econometric analysis, and system simulation to examine the mechanisms through which government subsidies influence collaborative innovation. Our baseline model estimates demonstrate that government subsidies have a significant positive effect on firms’ collaborative innovation capabilities, with notably stronger effects emerging in eastern regions and under specific market structures. Through mechanism analysis, this study identifies market structure as a critical mediating channel in the subsidy-innovation relationship, while digital infrastructure sophistication and market environment maturity serve as positive moderating factors. Moreover, panel analysis reveals that subsidies enhance both the immediate efficiency and long-term sustainability of innovation outputs. Simulation results derived from an enhanced NK model suggest that government subsidies optimize innovation system performance through dual mechanisms: increasing the optimal level of collaborative innovation and reducing performance fluctuations, though these effects exhibit systematic regional heterogeneity. By synthesizing multi-disciplinary perspectives, this paper develops an integrated analytical framework connecting government subsidies, market structure, and collaborative innovation, while systematically delineating the boundary conditions of subsidy effectiveness. These findings provide robust theoretical foundations and empirical evidence for precise policy design in emerging industries.