Green innovation of leading enterprises has a demonstration and radiation effect on promoting green and low-carbon development of enterprises. Based on resource orchestration and niche theory, this paper takes Shaanxi Coal and Chemical Industry Group, a state-owned leading enterprise, and LuBao Coking Group, a private leading enterprise, as case studies, analyzes the internal evolution mechanism of green innovation ecology of leading enterprises in traditional energy industry, and discusses the common characteristics and differentiated performance of leading enterprises with different ownership. The study makes three valuable findings. First, the ecological evolution of leading enterprises’ green innovation can be divided into three stages, dividing the time series interval by key events, and there are obvious differences in institutional logic, resource orchestration and behavior characteristics in different stages. Second, the key factors in the evolution of the green innovation ecology of leading enterprises are environmental response, resource orchestration, innovation ability and value creation. Through the synergy of key factors, the green innovation ecology of enterprises all embodies the common evolution process from state energy accumulation to potential energy improvement to suitability optimization. Third, under the constraints of multiple institutional logics, leading enterprises of different ownership systems show significant differences in the evolution of green innovation ecology: state-owned leading enterprises follow the innovative strategy of active response and promote the advancement of green innovation ecology through the innovation mechanism of “internal integration” of resources; however, private leading enterprises follow the innovation strategy of organizational adaptation, and promote the iterative evolution of green innovation ecology through the innovation mechanism of “extensional expansion” of resources. The conclusion mainly contributes that to promote the evolution of green innovation ecology from the perspective of leading enterprises based on “facilitating scenario-collaborative governance-evolution results”. It also explores new analysis dimensions from the differences in evolution logic, governance model and behavior characteristics between state-owned and private leading enterprises due to the different strategic orientations of green innovation. It provides theoretical support and management enlightenment for the leading enterprises in the traditional energy industry to promote the ecological upgrading of green innovation and achieve green and high-quality development.