Design thinking has developed for several decades, and we are an expert at applying human needs to innovation. However, the challenges that are currently rising with the acceleration to the Anthropocene, are beyond the scope of human-centered design thinking. Nature is losing its restoration capability, but the alternative solutions from the perspective of humans are inadequate to adapt to and protect the fluctuating environment. Thus, to solve the challenge, this study suggests an alternative design mode extracted from nature’s thinking process, Ecological model inspired thinking by transferring the underlying assumption of design thinking to biomimicry and multiple species-centered philosophy. A new ecological model for coexistent evolution has been developed and was used to design the steps and toolkits of the process. The effectiveness of the design mode was examined through comparative analysis with design thinking, exploring the potential for practical application of the new design scenario to present-day innovations.