Digitalization has reshaped the way of value co‐creation among innovation subjects, expanded the existing innovation ecosystem theories, and triggered the thinking about the digital innovation ecosystem. How to continuously promote value co‐creation between focal companies and non‐focal subjects within the digital innovation ecosystem to elevate the sustainable development of the system is an urgent issue to be solved. In this paper, we built a model of value co‐creation behavior evolution of focal companies and non‐focal subjects in the digital innovation ecosystem based on the complex network evolutionary game theory. The dynamic decision‐making process and critical factors of value co‐creation behavior of focal companies and non‐focal subjects were explored, and the emergence mechanism from micro‐behavior of value co‐creation to macro‐evolution was studied. The results showed that (1) increasing the variability of digital resources shared by focal companies and non‐focal subjects and the level of digital innovation benefits could promote value co‐creation in the system, but digital innovation ecosystems of different scales have various sensitivities to the variability of digital resources and the level of digital innovation benefits; (2) during the initial construction period of digital innovation ecosystems, the distribution of digital innovation benefits should be dominated by focal companies. With the expansion of the ecosystem, the focus of benefit distribution should gradually shift to non‐focal subjects. (3) In the evolution of the digital innovation ecosystem, focal companies should bear relatively more coordination costs of value co‐creation to promote the stable development of the system. (4) It is necessary to establish a punishment mechanism for opportunistic behavior, and the punishment should be gradually increased as the scale of digital innovation ecosystem expands. This study characterizes the digital innovation ecosystem with scale‐free networks in complex networks and constructs a complex network evolutionary game model to study the dynamic decision‐making process of value co‐creation behavior in the system, which makes up for the limitations of traditional evolutionary game research in which game subjects interact in a uniformly mixed manner and highlights the macroscopic phenomena emerging from the dynamic decision‐making of value co‐creation behavior of micro subjects. The research findings have important implications for the co‐creation of value by focal companies and non‐focal subjects in the digital innovation ecosystem and the sustainable development of the system.