Digital empowerment for green and low-carbon transformation and green innovation to pull digital leap is an important way for energy companies to realize sustainable development. The dynamic connection between heterogeneous subjects and the environment can accelerate the evolution of the dual synergistic development of digitalization and greening. Therefore, this paper analyzes the mechanism of "dual synergy" of the energy innovation system composed of energy enterprises, academics and researchers, and the government, constructs a three-party evolutionary game model and simulates it with MATLAB software, which shows that: the main body's willingness, the distribution of benefits, the liquidated damages, and the government's governance have different degrees of impacts on the dual synergy of the energy innovation system at different stages of digitization. The degree of influence of dualization synergy is different. Based on this, we propose the evolution strategy of "dualization synergy" for energy innovation system in different stages of digital transformation, in order to realize the highquality development of energy enterprises.