Abstract: In order to explore the main factors affecting agricultural carbon emission and differences between North and South China, agricultural carbon emissions in 31 provinces, autonomous regions and municipalities (Hong Kong, Macao and Taiwan not covered) were calculated based on relevant data and information available in the Agricultural Yearbooks of 1990-2014 concerning main sources of carbon input in agriculture, such as staple crops (wheat, rice and corn), pesticide, chemical fertilizer, plastic film, agricultural irrigation, farming machines and some others, for analysis of their affecting factors and regional differences in agricultural carbon emission intensity using the Kaya identical equation and Theil index, separately. Results show:(1) The agricultural carbon emission in China has been on a gradual upward trend in recent years. Some factors like the optimization of agricultural industrial structure can restrain the growth of agricultural carbon emissions. The development level of agricultural economy will promote the increase of agricultural carbon emissions. (2) In terms of spatial distribution, agricultural carbon emission is generally higher in the northern part of the country than in the southern. The intensity of agricultural carbon emission per unit of crop area is showing a rising tendency and that per unit of agricultural output a decreasing tendency. From the perspective of the regions per se, their Theil indices demonstrate that regional difference in agricultural carbon emission intensity primarily stemmed from inside of the regions. The difference in agricultural carbon emission intensity is greater in the southern part than in the northern and narrowing in the coastal areas in both parts. The differences within the northwest and southwest areas are gradually expanding. Some suggestions based on the above-listed findings are proposed.