In order to maximize the proportion of clean energy in rural areas and realize the clean and low-carbon transformation of the energy supply structure and energy consumption in rural areas, this paper proposes a clean scheduling strategy for the integrated rural energy system that takes into account the refined modeling of biogas digester waste heat feedback. Firstly, the mathematical model of coupling and interaction between biogas digester and integrated energy system heat flow is constructed to enhance the efficiency of energy utilization in rural areas; secondly, the carbon trading market is utilized to assist the construction of a clean and efficient multi-energy complementary system in rural areas to minimize the carbon emissions(CE) of the system, and the particle swarm algorithm guides the adaptive change of the carbon trading(CT) parameters to maximally tap the clean nature of the integrated energy system operation; finally, a variety of scenes are set for analysis, and the results show that the proposed scheme can reduce the CE of the system and improve the system operation economy to a certain extent.