Driven by the “dual carbon” goal, it is of great significance to realizethe effective synergy between green certificates and carbon markets to promotethe transformation of the energy structure. This study aims to explore howthe synergy between the green certificate market and the carbon market canaccelerate the low-carbon transition of the power sector in Guangdong Province.Firstly, the basic principle of synergy between carbon trading and greencertificate trading is analyzed, and then the role of green certificates in carbonemission reduction is discussed, and the equivalent interaction mechanism ofcarbon emission reductions corresponding to green certificate accounting isproposed, and then the system dynamics model is used to evaluate the impact ofdifferent carbon quota auction proportions on the energy structure of the power industry from 2020 to 2030 based on the actual data of Guangdong Provincein 2020. Finally, the simulation results show that the effective synergy betweengreen certificate and carbon market not only promotes the consumption ofrenewable energy and the low-carbon transformation of the energy structure,but also provides a reference for policymakers to strengthen the marketmechanism and policy support, aiming to optimize the energy structure andpromote the development of clean energy.