Continuous incorporation of rice straw has caused significant CH4 emissions from the paddy field production system in East China. Anaerobic digestion (AD) of the rice straw has been considered as a promising approach that could not only mitigate the land-based CH4 emissions, but also generate low-carbon electricity and high-quality organic fertilizer. However, this approach, in many circumstances, is unable to be cost-competitive with other straw treatment processes or power sources. To understand the potential incentives that recently launched carbon trading schemes, the China Carbon Emission Trade Exchange (CCETE) and Chinese Certified Emission Reduction (CCER), could bring to the rice straw utilization value chain, we conducted a cradle-to-factory gate life cycle assessment and economic analysis of a small-scale AD system with rice straw as the main feedstock in East China. The results indicate that, depending on the choice of allocation method, the climate change impact of the bioenergy generated through the studied small-scale AD system is 0.21 to 0.28 kg CO2eq./kWh, and the digester fertilizer produced is 6.88 to 22.09 kg CO2eq./kg N. The economic analysis validates the financial sustainability of such small-scale AD projects with rice straw feedstock under carbon trading mechanisms. The climate mitigation potential could be achieved at the marginal reduction cost of 13.98 to −53.02 USD/t CO2eq. in different carbon price scenarios.