At present, the world economy is facing severe challenges such as climate deterioration and limited energy resources. It is an inevitable requirement and an effective path to build a clean and low-carbon energy system to accelerate the dual replacement process of the energy structure of “oil and gas replacing coal and non-fossil energy replacing fossil energy”. In December 2020, the State Council Information Office released the white paper ,titled “Energy in China's New Era” , emphasizing the need to “deeply implement the innovation-driven development strategy, build a green energy technology innovation system, and comprehensively improve the level of energy technology and equipment”, which indicates that the energy development has entered an innovation-driven stage in China. Can current technological innovation effectively promote the transformation and development of the energy structure? Can the innovation path that drives the adjustment of the energy structure be further optimized? The above problems are crucial to solving energy and environmental constraints and achieving sustainable development.#br#By constructing a game model of government innovation investment and enterprise innovation investment, this paper analyzed four situations in the process of government-market collaborative innovation, including risk-averse and defensive formation, policy-guided, market-driven and collaborative. Further, on the basis of the provincial sample data from 2009 to 2019, a threshold regression model is used to empirically test the impact of government and enterprise innovation investment on energy structure substitution at each stage, and the threshold value is used as the dividing line to group 30 provinces in mainland China in the discussion of the transformation of regional energy structure in different government-market collaborative innovation models.#br#The data is from the China Statistical Yearbook, China Energy Statistical Yearbook, China Science and Technology Statistical Yearbook, China Economic Census Yearbook and regional statistical yearbooks over the years. The sample study period is from 2009 to 2019, and the research objects include 30 provinces and cities in China (excluding Tibet, Hong Kong, Macao and Taiwan due to missing data). The data involving price changes were deflated with 2009 as the base period.#br#It is found that (1) government innovation support and increased corporate R&D investment generally have a significant positive effect on the replacement of coal by oil and gas, the replacement of fossil energy by non-fossil energy, and the dual replacement process of energy structure; (2) the effect of government and enterprise innovation input on energy structure substitution shows strong heterogeneity among different regions, and the government-market collaborative innovation in the central and western regions has a significant negative impact on the energy structure substitution process; (3) with the increasing investment in innovation by the government and enterprises, the positions of the government and enterprises in the process of promoting the transformation of the energy structure are constantly changing, but the overall coordination between the government and enterprises is always at a low level, failing to exert a positive synergy effect of “1+1>2”; (4) in the process of replacing coal with oil and gas and the dual replacement of energy structure，most provinces are still taking hedging and preventive measures and the government and enterprises are not motivated to invest in innovation.#br#This paper provides ideas for further in-depth research in the future. (1) It mainly examines the impact of government-market collaborative innovation on energy structure substitution from a static perspective. Although the explanatory variables with a lag of one period are introduced in the robustness test part for discussion, there is still a lack of systematic investigation from a dynamic perspective, which can be supplemented and improved. (2) In addition to enterprises and government departments, participants in innovation activities also include universities and scientific research institutions. With limited data, this study only starts with the interaction between the government and the market, and explores the relationship between government-enterprise collaborative innovation and energy structure transformation. With the deepening of government-industry-university-research cooperation, it is possible to further build a four-sector game model of government, market, universities and scientific research institutions in the future to investigate the driving effect of multi-sectoral collaborative innovation on energy structure transformation. (3) Although government-market collaborative innovation is confirmed to have a significant impact on the transformation of energy structure, the specific path and mechanism of this impact are still unclear, and further research is expected.#br#