Exploring agricultural production efficiency under the constraint of carbon emissions based on village scale not only helps to reveal the relationship between carbon emission at the micro unit level and agricultural production efficiency, but also has certain practical significance for the choice of differentiated low-carbon agricultural production mode. Based on the survey data obtained from 65 villages in Henan province, this paper calculated the agricultural carbon emission at different sample villages, and analyzed differences in agricultural production efficiency under the constraint of carbon emission using Super-SBM model. The results show that: (1) The spatial distribution pattern of agricultural carbon emission intensity in the study area is "high in the north and south, but low in the middle", which is mainly affected by planting structure, agricultural production conditions, and human inputs. (2) Intensive use and large-scale operation of land will reduce the energy and material input per unit area, thereby reducing agricultural carbon emission intensity. (3) There are great spatial differences in agricultural production efficiency under the constraint of carbon emissions. The average agricultural production efficiency of the sample villages is 0.76, and the most areas are between 0.6 and 0.8. (4) According to the relationship between agricultural production efficiency and carbon emission intensity, the sample villages can be divided into four types: low carbon and high efficiency villages, high carbon and low efficiency villages, high carbon and high efficiency villages and low carbon and low efficiency villages. Among them, the two types of high carbon and low carbon inefficient villages account for a large proportion, which indicates that there is a widespread problem of low agricultural production efficiency in Henan. In the future, we should strengthen large-scale agricultural operations, reduce energy and material input, improve agricultural infrastructure, and advance new technologies for water saving and energy conservation, so as to promote the low-carbon development of agriculture while improving the efficiency of agricultural production.