Dual carbon target is the definition of carbon peak and carbon neutrality, on the one hand reducing fossil consumption in order to reduce carbon emissions, and on the other hand using afforestation to increase carbon absorption. In recent years, Sichuan ethnic areas actively implemented the “double carbon” strategy, committed to promoting the low-carbon development of agriculture. In this paper, the agricultural carbon emissions of Sichuan ethnic areas from 2006 to 2021 were measured, and then the efficiency was calculated by the super-efficiency SBM model and the influencing factors were calculated by the Tobit model. The results show that the agricultural carbon emissions in ethnic areas of Sichuan show an increasing trend, with the carbon emissions in Liangshan Prefecture being the largest, and its increase is also the largest. Agricultural carbon emission efficiency showed a fluctuating trend and gradually changed to the effective state, but the efficiency in Ganzi Prefecture was the lowest in 2021. Agricultural mechanization level, agricultural economic development level, and farmland irrigation rate can promote agricultural carbon emission efficiency, while fertilizer application rate has a negative effect on it. Based on this, the paper puts forward some suggestions on the scientific use of chemical fertilizers, the vigorous implementation of water-saving actions, the emphasis on improving farmers’ environmental awareness, the transformation and upgrading of agriculture, and the optimization of agricultural industrial structures and agricultural products.