In the digital innovation ecosystem, the symbiosis mode formed between ecosystem members not only relates to their survival and development but also affects the ecosystem’s symbiosis evolution mechanism. Based on symbiosis theory, this study first explores the evolutionary equilibrium strategy and its stability for three types of populations—core enterprises, digital platforms, and university research institutes—and then uses numerical simulation and a case study to explore the symbiotic evolution mechanism of the digital innovation ecosystem. The results show that: First, the digital innovation ecosystem is a complex adaptive system in which the three types of populations form different symbiotic relationships under different symbiotic modes and conduct symbiotic activities, such as value co-creation, to characterize the unique symbiotic evolutionary structure. Second, in this ecosystem, the symbiotic relationship formed by the combined values of different symbiotic coefficients between populations determines the outcome of symbiotic evolution. Third, the ideal direction of the evolution of the digital innovation ecosystem is a mutually beneficial symbiotic relationship. Thus, the symbiotic relationship between populations should be transformed into a mutually beneficial symbiotic relationships as much as possible. This study makes theoretical contributions by shedding light on the symbiotic evolution mechanism of the digital innovation ecosystem. It also offers countermeasures for the digital innovation cooperation of various stakeholders in China’s digital innovation ecosystem.