Abstract: Low-carbon agricultural production is the key to achieving green and high-quality agricultural development. The main grain-producing area is an important guarantee of national food security and the main area of the agricultural carbon emissions in China. Thus, exploring the degree of coupling and coordination between low-carbon agricultural systems is warranted to carry out the coordinated and balanced development of low-carbon agriculture in the major grain-producing areas. This study used the super-efficient SBM model to measure the agricultural carbon emission efficiency of 13 provinces (autonomous regions) in the major grain-producing areas of China, covering the Songhua, Yellow, and Yangtze River basins from 2001 to 2021. A low-carbon agricultural evaluation system of agricultural carbon emissions, agricultural economic development, and agroecological environment was constructed, which included the efficiency of agricultural carbon emissions. The coupling coordination model was adopted to measure the degree of coupling coordination between low-carbon agricultural systems in the major grain-producing areas to explore the spatial and temporal patterns of the coordinated evolution of each system. The results showed that: 1) the average value of agricultural carbon emission efficiency in the major grain-producing areas of China showed a fluctuating upward trend from 2001 to 2021, with the highest average value of 0.964 in 2021. The average value of agricultural carbon emission efficiency increased sharply during the period of study, but the average value remained lower than 1, which did not meet the optimal production frontiers. In terms of provincial differences in 2021, only Anhui and Hunan provinces in the major grain-producing areas did not reach the effective state of agricultural carbon emission efficiency. Liaoning Province had the highest level of agricultural carbon emission efficiency of 1.184, and Anhui Province had the lowest level of 0.522. The average value of agricultural carbon emission efficiency from high to low were Songhua River Basin > Yellow River Basin > Yangtze River Basin. This resulted in a significant difference in the level of agricultural carbon emission efficiency among the provinces. 2) From 2001 to 2021, the overall coupling and coordination degree of low-carbon agricultural systems in the major grain-producing areas showed a steady growth trend, and the coupling and coordination level was in the stage of coordinated development, which was still a certain distance away from high-quality coordination. During the study period, the coupling degree of coordination between low-carbon agricultural systems in the provinces was between 0.6 and 0.9, and showed a clear upward trend. The degree of coupling coordination went through development stage of primary coordination, intermediate coordination, to good coordination, but large differences were observed between provinces. The degree of coupling coordination showed a trend of “high in the north and low in the south” and “high in the east and low in the west”. Based on this, the following three countermeasures were proposed: first, strengthen inter-regional cooperation to jointly promote the development of low-carbon agriculture; second, implement the new concept of low-carbon production and continuously improve the low-carbon awareness of farmers; and third, strengthen the agricultural science and technology innovation, and continuously improve the agricultural carbon emission reduction technology.