Developing low-carbon agriculture can effectively avoid the waste of natural resources, thus contributing to the long-term sustainability of agriculture. This study uses the Super-SBM model to measure agricultural low-carbon economic efficiency (ALEE) in China from 2000 to 2018, then analyzes the spatial-temporal evolution characteristics. Simultaneously, the influencing factors of ALEE are investigated using spatial econometric model. The results show that: (1) In terms of temporal evolution, the ALEE in most provinces is declined over time, with only a few provinces improving. The ALEE in China and the three regions all show an obvious “L” trend of decline first and then stability. (2) From the perspective of spatial differentiation, provinces in eastern region have higher ALEE, while those in central and western regions have lower ALEE. Hainan’s ALEE has an absolute advantage, while Shanxi is the worst. (3) China’s ALEE shows obvious spatial agglomeration characteristics of H-H and L-L agglomeration, which are further enhanced over time. The number of L-L agglomeration provinces gradually increases, indicating that China’s ALEE has not been improved significantly. (4) Economic growth level and Agricultural scientific and Technological progress have effectively improved the ALEE. However, Capital deepening, Government fiscal expenditure, Agricultural planting structure, and Agricultural disaster all have negative impacts. Rural electricity consumption also has a negative impact, but the impact is not significant. To accelerate the development of low-carbon agriculture, all regions must not only pursue a differentiated low-carbon agriculture development path, but also accelerate agricultural transformation, strengthen research and development, and popularize low-carbon agricultural technologies, reduce the input of traditional agricultural means of production, optimize the agricultural industrial structure, and adjust agricultural subsidy policies.