In recent years, green innovation has gained substantial attention and popularity from the manufacturing industry around the world. As an essential part of the manufacturing industry, small and medium-sized manufacturing enterprises (SMMEs) are vital participants that promote green innovation to realize sustainable development. However, how green innovation evolves in SMMEs is unclear, which hinders SMMEs from implementing or even adopting green innovation. This study attempted to essentially reveal the evolution of green innovation in SMMEs based on complex systems theory. First, this study divided green innovation into green product innovation and green process innovation, defined the state variables of the two components, and dissected the symbiotic interactions between them. This study then designed a nonlinear dynamic model followed by extensive simulations to theoretically and visually describe how green innovation evolves. This study found that green innovation with non-zero levels in both dimensions is desired and determines the evolutionary paths with corresponding measures that can guide SMMEs to realize green innovation at desired stable states. Besides, symmetric mutualism is discovered to be the optimal symbiotic interaction. Based on these findings, regulatory subjects and SMMEs can duly adjust the inputs on green innovation and the symbiotic interactions within green innovation to better manage green innovation practices.