The study of the carbon emission intensity of agricultural production is of great significance for the formulation of a rational agricultural carbon reduction policy. This paper examines the regional differences, spatial–temporal pattern and dynamic evolution of the carbon emission intensity of agriculture production from 1991 to 2018 through the Theil index and spatial data analysis. The results are shown as follows: The overall differences in carbon emission intensity of agriculture production presents a slightly enlarging trend, while the inter-regional differences in carbon emissions intensity is decreasing, but the intra-regional difference of carbon emissions intensity presented an expanding trend. The difference in carbon emission intensity between the eastern and central regions is not obvious, and the difference in carbon emission intensity in the western region shows a fluctuating and increasing trend. The overall differences caused by intra-regional differences; the average annual contribution of intra-regional differences is 67.84%, of which the average annual contribution of western region differences is 64.24%. The carbon emission intensity of agricultural production in China shows a downward trend, with provinces with high carbon emission intensity remaining stable, while provinces with low intensity are expanding. The Global Moran’s I index indicates that China’s carbon emission intensity of agricultural production shows a clear trend of spatial aggregation. The agglomeration trend of high agricultural carbon emission remains stable, and the overall pattern of agricultural carbon emission intensity shows a pattern of increasing differentiation from east to west.