The rural multi-energy system (RMES) can effectively advance the energy transition in rural areas and holds the potential to enhance economic and environmental benefits. Nevertheless, the existing rural energy systems fail to fully account for the coupled utilization of energy equipment and lack consideration of the impacts of market policies. This paper proposes a low-carbon economic optimization model that takes into account the combined operation of pyrolysis equipment and biogas digesters, the coupling mechanism of carbon emission trading (CET) and green certificate trading (GCT), as well as life-cycle environmental assessment. Firstly, an operation framework of RMES based on the joint operation of pyrolysis devices and biogas digesters is constructed to clarify the coupling relationships among various energy flows and equipments. Secondly, a coupled market trading mechanism integrating carbon and green certificates is introduced to raise the utilization rate of renewable energy via market regulation. Thirdly, a life cycle assessment (LCA) procedure for the system is established with environmental factors taken into consideration, which quantifies carbon emissions and standard pollutant discharges at different stages and incorporates these indicators into the model optimization system. Finally, comparative analysis is conducted through numerical examples under multiple scenarios. The results demonstrate that the proposed method can effectively boost environmental benefits, facilitate the consumption of renewable energy and improve the economic performance of the system.